Datasets:

bolinas-dna
/

evals_complex_traits

chrom stringclasses 12 values	pos int64 36.1k 249M	ref stringclasses 4 values	alt stringclasses 4 values	label bool 2 classes	subset stringclasses 8 values	match_group int64 0 2.16k	rsid stringlengths 3 15	pip float64 0 1	traits stringclasses 279 values	MAF float64 0 0.5	ld_score float64 1.01 3.79k	consequence stringclasses 13 values	consequence_cre stringclasses 29 values	exon_closest_pc_gene_id stringlengths 15 15	distance_exon_pc int64 0 1.68M	exon_closest_nc_gene_id stringlengths 15 15	distance_exon_nc int64 0 507k	distance_exon int64 0 507k	exon_closest_gene_id stringlengths 15 15	consequence_final stringclasses 28 values	tss_closest_pc_gene_id stringlengths 15 15	distance_tss_pc int64 0 1.69M	tss_closest_nc_gene_id stringlengths 15 15	distance_tss_nc int64 0 531k	distance_tss int64 0 531k	tss_closest_gene_id stringlengths 15 15	consequence_group stringclasses 8 values	distance_tss_pc_bin stringclasses 4 values	distance_exon_pc_bin stringclasses 7 values
1	868,052	T	C	false	non_coding_transcript_exon_variant	116	rs562238357	0.002114		0.077747	44.057	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000187634	55,870	ENSG00000288531	0	0	ENSG00000288531	non_coding_transcript_exon_variant	ENSG00000187634	55,870	ENSG00000230368	2,148	2,148	ENSG00000230368	non_coding_transcript_exon_variant	NA	NA
1	868,635	A	G	false	non_coding_transcript_exon_variant	116	rs372466154	0.00435		0.075255	43.639	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000187634	55,287	ENSG00000230368	0	0	ENSG00000230368	non_coding_transcript_exon_variant	ENSG00000187634	55,287	ENSG00000230368	1,565	1,565	ENSG00000230368	non_coding_transcript_exon_variant	NA	NA
1	870,176	T	A	false	non_coding_transcript_exon_variant	116	rs72631880	0.000335		0.084371	37.271	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000187634	53,746	ENSG00000230368	0	0	ENSG00000230368	non_coding_transcript_exon_variant	ENSG00000187634	53,746	ENSG00000230368	24	24	ENSG00000230368	non_coding_transcript_exon_variant	NA	NA
1	953,778	G	C	false	splicing	168	rs13303056	0.00015		0.05337	66.508	splice_donor_region_variant	splice_donor_region_variant	ENSG00000188976	3	ENSG00000188976	3	3	ENSG00000188976	splice_donor_region_variant	ENSG00000188976	5,477	ENSG00000188976	4,679	4,679	ENSG00000188976	splicing	NA	splicing:b0
1	953,779	A	C	false	splicing	168	rs13302945	0.000194		0.05329	65.877	splice_donor_region_variant	splice_donor_region_variant	ENSG00000188976	2	ENSG00000188976	2	2	ENSG00000188976	splice_donor_region_variant	ENSG00000188976	5,476	ENSG00000188976	4,678	4,678	ENSG00000188976	splicing	NA	splicing:b0
1	973,858	G	C	false	missense_variant	101	rs3829740	0.000941		0.43173	37.076	missense_variant	missense_variant	ENSG00000187583	0	ENSG00000187642	1,346	0	ENSG00000187583	missense_variant	ENSG00000187583	345	ENSG00000187642	2,782	345	ENSG00000187583	missense_variant	NA	NA
1	973,929	T	C	false	missense_variant	93	rs3829738	0.0097		0.17172	64.661	missense_variant	missense_variant	ENSG00000187583	0	ENSG00000187642	1,275	0	ENSG00000187583	missense_variant	ENSG00000187583	416	ENSG00000187642	2,711	416	ENSG00000187583	missense_variant	NA	NA
1	1,043,382	G	A	false	missense_variant	78	rs138288952	0.001138		0.012424	10.869	missense_variant	missense_variant	ENSG00000188157	0	ENSG00000188157	1,984	0	ENSG00000188157	missense_variant	ENSG00000188157	9,275	ENSG00000188157	2,016	2,016	ENSG00000188157	missense_variant	NA	NA
1	1,118,290	G	A	false	distal	57	rs4970410	0.000247		0.13637	125.81	intergenic_variant	dELS	ENSG00000131591	1,928	ENSG00000131591	2,046	1,928	ENSG00000131591	dELS	ENSG00000131591	1,928	ENSG00000131591	2,046	1,928	ENSG00000131591	distal	NA	NA
1	1,118,344	A	G	false	distal	57	rs4970411	0.000262		0.1362	125.78	intergenic_variant	dELS	ENSG00000131591	1,982	ENSG00000131591	2,100	1,982	ENSG00000131591	dELS	ENSG00000131591	1,982	ENSG00000131591	2,100	1,982	ENSG00000131591	distal	NA	NA
1	1,129,916	T	C	true	distal	0	rs4072537	0.992915	P	0.319	33.097	intergenic_variant	dELS_flank	ENSG00000131591	13,554	ENSG00000223823	7,100	7,100	ENSG00000223823	dELS_flank	ENSG00000131591	13,554	ENSG00000223823	7,100	7,100	ENSG00000223823	distal	NA	NA
1	1,179,830	G	A	false	5_prime_UTR_variant	124	rs11260546	0.000126		0.11464	27.348	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000162571	0	ENSG00000205231	274	0	ENSG00000162571	5_prime_UTR_variant	ENSG00000162571	132	ENSG00000205231	274	132	ENSG00000162571	5_prime_UTR_variant	NA	NA
1	1,179,833	G	T	false	5_prime_UTR_variant	124	rs11260547	0.000125		0.11451	27.317	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000162571	0	ENSG00000205231	277	0	ENSG00000162571	5_prime_UTR_variant	ENSG00000162571	135	ENSG00000205231	277	135	ENSG00000162571	5_prime_UTR_variant	NA	NA
1	1,180,847	G	A	false	missense_variant	72	rs200208314	0.000086		0.003645	3.529	missense_variant	missense_variant	ENSG00000162571	0	ENSG00000162571	0	0	ENSG00000162571	missense_variant	ENSG00000162571	1,149	ENSG00000162571	309	309	ENSG00000162571	missense_variant	NA	NA
1	1,195,347	A	C	false	distal	24	rs10907175	0.000085		0.097481	125.16	intron_variant	dELS_flank	ENSG00000162571	1,252	ENSG00000162571	1,038	1,038	ENSG00000162571	dELS_flank	ENSG00000186891	10,332	ENSG00000162571	10,310	10,310	ENSG00000162571	distal	NA	NA
1	1,197,558	G	A	false	missense_variant	89	rs2274791	0.000043		0.1057	65.704	missense_variant	missense_variant	ENSG00000162571	0	ENSG00000162571	82	0	ENSG00000162571	missense_variant	ENSG00000186891	8,121	ENSG00000162571	12,521	8,121	ENSG00000186891	missense_variant	NA	NA
1	1,211,644	G	A	false	missense_variant	79	rs34945898	0.00023		0.008409	43.564	missense_variant	missense_variant	ENSG00000186827	0	ENSG00000186827	0	0	ENSG00000186827	missense_variant	ENSG00000186827	2,508	ENSG00000186827	1,853	1,853	ENSG00000186827	missense_variant	NA	NA
1	1,217,251	C	A	false	3_prime_UTR_variant	133	rs11721	0.000102		0.090388	168.84	3_prime_UTR_variant	3_prime_UTR_variant	ENSG00000078808	0	ENSG00000078808	0	0	ENSG00000078808	3_prime_UTR_variant	ENSG00000186827	3,097	ENSG00000078808	3,041	3,041	ENSG00000078808	3_prime_UTR_variant	NA	NA
1	1,222,957	C	T	false	distal	7	rs778736306	0.000125		0.001049	17.49	intron_variant	dELS_flank	ENSG00000078808	286	ENSG00000078808	286	286	ENSG00000078808	dELS_flank	ENSG00000078808	5,638	ENSG00000078808	1,605	1,605	ENSG00000078808	distal	NA	NA
1	1,262,318	T	C	false	missense_variant	99	rs72631900	0.000327		0.039887	32.604	missense_variant	missense_variant	ENSG00000160087	1,027	ENSG00000160087	0	0	ENSG00000160087	missense_variant	ENSG00000160087	11,152	ENSG00000160087	1,250	1,250	ENSG00000160087	missense_variant	NA	NA
1	1,291,864	G	A	false	3_prime_UTR_variant	135	rs2239609	0.000373		0.049257	79.498	3_prime_UTR_variant	3_prime_UTR_variant	ENSG00000162572	0	ENSG00000162572	490	0	ENSG00000162572	3_prime_UTR_variant	ENSG00000162572	4,754	ENSG00000131584	3,143	3,143	ENSG00000131584	3_prime_UTR_variant	NA	NA
1	1,336,473	G	C	false	missense_variant	87	rs113005319	0.000544		0.019135	17.269	missense_variant	missense_variant	ENSG00000107404	0	ENSG00000107404	1,860	0	ENSG00000107404	missense_variant	ENSG00000107404	2,948	ENSG00000284372	3,234	2,948	ENSG00000107404	missense_variant	NA	NA
1	1,370,181	C	T	false	distal	45	rs17160669	0.009015		0.12415	193.14	intergenic_variant	dELS	ENSG00000175756	3,548	ENSG00000175756	4,062	3,548	ENSG00000175756	dELS	ENSG00000175756	4,975	ENSG00000175756	4,962	4,962	ENSG00000175756	distal	NA	NA
1	1,370,317	G	C	false	distal	45	rs111421264	0.008489		0.12415	193.15	intergenic_variant	dELS	ENSG00000175756	3,412	ENSG00000175756	3,926	3,412	ENSG00000175756	dELS	ENSG00000175756	4,839	ENSG00000175756	4,826	4,826	ENSG00000175756	distal	NA	NA
1	1,370,320	A	G	false	distal	45	rs113429154	0.008526		0.12415	193.15	intergenic_variant	dELS	ENSG00000175756	3,409	ENSG00000175756	3,923	3,409	ENSG00000175756	dELS	ENSG00000175756	4,836	ENSG00000175756	4,823	4,823	ENSG00000175756	distal	NA	NA
1	1,370,430	T	C	false	distal	45	rs35194784	0.00625		0.12421	193.12	intergenic_variant	dELS	ENSG00000175756	3,299	ENSG00000175756	3,813	3,299	ENSG00000175756	dELS	ENSG00000175756	4,726	ENSG00000175756	4,713	4,713	ENSG00000175756	distal	NA	NA
1	1,370,584	G	C	false	distal	45	rs34457386	0.007965		0.1237	193.19	intergenic_variant	dELS	ENSG00000175756	3,145	ENSG00000175756	3,659	3,145	ENSG00000175756	dELS	ENSG00000175756	4,572	ENSG00000175756	4,559	4,559	ENSG00000175756	distal	NA	NA
1	1,375,267	C	T	false	tss_proximal	172	rs139833628	0.000981		0.017245	144.08	upstream_gene_variant	pELS	ENSG00000175756	59	ENSG00000175756	107	59	ENSG00000175756	tss_proximal	ENSG00000175756	59	ENSG00000175756	107	59	ENSG00000175756	tss_proximal	tss_prox:b0	tss_prox:b0
1	1,399,139	G	C	false	missense_variant	82	rs114112990	0.000531		0.017196	142.97	missense_variant	missense_variant	ENSG00000221978	0	ENSG00000221978	0	0	ENSG00000221978	missense_variant	ENSG00000221978	177	ENSG00000221978	169	169	ENSG00000221978	missense_variant	NA	NA
1	1,426,810	C	G	false	tss_proximal	138	rs1781137	0.002184		0.21956	182.49	intron_variant	pELS	ENSG00000205116	424	ENSG00000225285	3,728	424	ENSG00000205116	tss_proximal	ENSG00000205116	938	ENSG00000225285	5,032	938	ENSG00000205116	tss_proximal	tss_prox:b1	tss_prox:b1
1	1,485,073	G	A	false	missense_variant	113	rs150679247	0.000123		0.000216	6.338	missense_variant	missense_variant	ENSG00000160072	0	ENSG00000160072	0	0	ENSG00000160072	missense_variant	ENSG00000160072	13,288	ENSG00000160072	503	503	ENSG00000160072	missense_variant	NA	NA
1	1,527,777	G	C	false	missense_variant	76	rs78493114	0.00017		0.000049	66.56	missense_variant	missense_variant	ENSG00000197785	0	ENSG00000197785	0	0	ENSG00000197785	missense_variant	ENSG00000197785	3,821	ENSG00000197785	10,155	3,821	ENSG00000197785	missense_variant	NA	NA
1	1,534,019	T	C	false	missense_variant	75	rs41285842	0.000092		0.013097	6.8587	missense_variant	missense_variant	ENSG00000197785	0	ENSG00000197785	0	0	ENSG00000197785	missense_variant	ENSG00000205090	6,330	ENSG00000160075	12,467	6,330	ENSG00000205090	missense_variant	NA	NA
1	1,662,855	T	C	false	3_prime_UTR_variant	135	rs1061892	0.00624		0.05362	40.356	3_prime_UTR_variant	3_prime_UTR_variant	ENSG00000189339	0	ENSG00000272004	252	0	ENSG00000189339	3_prime_UTR_variant	ENSG00000248333	3,842	ENSG00000272004	3,529	3,529	ENSG00000272004	3_prime_UTR_variant	NA	NA
1	1,703,572	A	G	false	missense_variant	99	rs866149312	0.000111		0.033949	121.68	missense_variant	missense_variant	ENSG00000008128	0	ENSG00000008128	0	0	ENSG00000008128	missense_variant	ENSG00000189339	10,776	ENSG00000008128	543	543	ENSG00000008128	missense_variant	NA	NA
1	1,916,540	T	C	false	missense_variant	81	rs28581776	0.000137		0.036122	141.78	missense_variant	missense_variant	ENSG00000169885	0	ENSG00000169885	0	0	ENSG00000169885	missense_variant	ENSG00000169885	1,279	ENSG00000169885	1,130	1,130	ENSG00000169885	missense_variant	NA	NA
1	1,927,737	T	C	false	missense_variant	99	rs45489198	0.000157		0.036242	142.24	missense_variant	missense_variant	ENSG00000142609	0	ENSG00000142609	0	0	ENSG00000142609	missense_variant	ENSG00000178821	8,457	ENSG00000142609	191	191	ENSG00000142609	missense_variant	NA	NA
1	2,025,598	T	C	false	missense_variant	74	rs2229110	0.000093		0.34716	48.343	missense_variant	missense_variant	ENSG00000187730	0	ENSG00000187730	0	0	ENSG00000187730	missense_variant	ENSG00000187730	71	ENSG00000187730	929	71	ENSG00000187730	missense_variant	NA	NA
1	2,025,744	C	T	false	splicing	169	rs202225187	0.000106		0.0014	14.028	splice_donor_region_variant	splice_donor_region_variant	ENSG00000187730	5	ENSG00000187730	0	0	ENSG00000187730	splice_donor_region_variant	ENSG00000187730	217	ENSG00000187730	783	217	ENSG00000187730	splicing	NA	splicing:b1
1	2,056,854	G	C	false	distal	7	rs2678953	0.000643		0.001462	83.56	intron_variant	dELS_flank	ENSG00000067606	280	ENSG00000067606	280	280	ENSG00000067606	dELS_flank	ENSG00000067606	6,045	ENSG00000067606	1,174	1,174	ENSG00000067606	distal	NA	NA
1	2,056,874	G	C	false	distal	7	rs2803315	0.000758		0.001715	76.522	intron_variant	dELS_flank	ENSG00000067606	300	ENSG00000067606	300	300	ENSG00000067606	dELS_flank	ENSG00000067606	6,065	ENSG00000067606	1,194	1,194	ENSG00000067606	distal	NA	NA
1	2,056,929	C	G	false	distal	7	rs2803317	0.000586		0.001493	82.588	intron_variant	dELS_flank	ENSG00000067606	355	ENSG00000067606	355	355	ENSG00000067606	dELS_flank	ENSG00000067606	6,120	ENSG00000067606	1,249	1,249	ENSG00000067606	distal	NA	NA
1	2,056,930	G	A	false	distal	7	rs150364419	0		0.000176	24.056	intron_variant	dELS_flank	ENSG00000067606	356	ENSG00000067606	356	356	ENSG00000067606	dELS_flank	ENSG00000067606	6,121	ENSG00000067606	1,250	1,250	ENSG00000067606	distal	NA	NA
1	2,107,293	C	T	false	distal	29	rs12410859	0.003341		0.27064	157.37	intron_variant	dELS	ENSG00000067606	2,397	ENSG00000067606	24,832	2,397	ENSG00000067606	dELS	ENSG00000067606	2,553	ENSG00000067606	25,044	2,553	ENSG00000067606	distal	NA	NA
1	2,181,226	G	A	false	distal	11	rs262691	0.000478		0.37595	161.8	intron_variant	dELS_flank	ENSG00000162585	3,234	ENSG00000182873	567	567	ENSG00000182873	dELS_flank	ENSG00000162585	13,521	ENSG00000182873	2,648	2,648	ENSG00000182873	distal	NA	NA
1	2,293,397	G	A	true	distal	26	rs12743493	0.99993	Height	0.37057	32.302	intron_variant	dELS	ENSG00000157933	9,580	ENSG00000157933	9,580	9,580	ENSG00000157933	dELS	ENSG00000157933	65,077	ENSG00000157933	10,248	10,248	ENSG00000157933	distal	NA	NA
1	2,383,999	G	A	false	distal	57	rs2645060	0.000616		0.13539	30.843	intron_variant	dELS	ENSG00000116151	978	ENSG00000116151	978	978	ENSG00000116151	dELS	ENSG00000116151	4,337	ENSG00000116151	1,121	1,121	ENSG00000116151	distal	NA	NA
1	2,408,134	G	T	false	distal	40	rs79338697	0.000323		0.024474	20.743	intron_variant	dELS	ENSG00000157911	317	ENSG00000157911	317	317	ENSG00000157911	dELS	ENSG00000157911	4,405	ENSG00000157911	1,869	1,869	ENSG00000157911	distal	NA	NA
1	2,467,425	C	G	false	tss_proximal	173	rs34349643	0.00007		0.1091	51.566	intron_variant	PLS	ENSG00000149527	33	ENSG00000149527	11,664	33	ENSG00000149527	tss_proximal	ENSG00000149527	33	ENSG00000149527	11,664	33	ENSG00000149527	tss_proximal	tss_prox:b0	tss_prox:b0
1	2,544,035	C	T	false	distal	64	rs55929178	0.00027		0.22511	132.11	intron_variant	dELS	ENSG00000157873	11,603	ENSG00000272449	1,933	1,933	ENSG00000272449	dELS	ENSG00000157873	11,603	ENSG00000272449	2,314	2,314	ENSG00000272449	distal	NA	NA
1	2,556,959	C	T	false	tss_proximal	136	rs142945923	0.000138		0.014056	179.64	intron_variant	PLS	ENSG00000157873	225	ENSG00000238164	17	17	ENSG00000238164	tss_proximal	ENSG00000157873	587	ENSG00000238164	71	71	ENSG00000238164	tss_proximal	tss_prox:b1	tss_prox:b1
1	2,591,979	C	T	false	missense_variant	80	rs141763894	0.000111		0.000558	3.0821	missense_variant	missense_variant	ENSG00000142606	0	ENSG00000142606	0	0	ENSG00000142606	missense_variant	ENSG00000142606	698	ENSG00000142606	888	698	ENSG00000142606	missense_variant	NA	NA
1	3,033,425	A	C	false	distal	29	rs376327715	0.000987		0.25335	151.8	intergenic_variant	dELS	ENSG00000169717	10,521	ENSG00000177133	26,185	10,521	ENSG00000169717	dELS	ENSG00000169717	11,957	ENSG00000177133	28,325	11,957	ENSG00000169717	distal	NA	NA
1	3,080,038	T	C	true	distal	27	rs1569419	0.999895	MCH,MCV,Plt,RBC	0.23272	31.606	intron_variant	dELS	ENSG00000142611	10,741	ENSG00000142611	10,741	10,741	ENSG00000142611	dELS	ENSG00000142611	10,826	ENSG00000142611	10,854	10,826	ENSG00000142611	distal	NA	NA
1	3,309,975	T	A	false	non_coding_transcript_exon_variant	119	rs59127130	0.000122		0.044983	42.36	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000142611	65,837	ENSG00000272235	0	0	ENSG00000272235	non_coding_transcript_exon_variant	ENSG00000142611	65,842	ENSG00000272235	120	120	ENSG00000272235	non_coding_transcript_exon_variant	NA	NA
1	3,388,532	G	C	false	distal	15	rs55792473	0.000208		0.14042	30.03	intron_variant	dELS_flank	ENSG00000142611	1,613	ENSG00000142611	3,245	1,613	ENSG00000142611	dELS_flank	ENSG00000142611	7,958	ENSG00000286518	14,603	7,958	ENSG00000142611	distal	NA	NA
1	3,473,193	A	G	true	missense_variant	72	rs41315284	1	eGFRcys	0.004783	2.4413	missense_variant	missense_variant	ENSG00000130762	0	ENSG00000130762	0	0	ENSG00000130762	missense_variant	ENSG00000130762	1,568	ENSG00000130762	423	423	ENSG00000130762	missense_variant	NA	NA
1	3,490,443	G	A	false	3_prime_UTR_variant	133	rs2821039	0.000235		0.09513	72.902	3_prime_UTR_variant	3_prime_UTR_variant	ENSG00000162591	0	ENSG00000162591	0	0	ENSG00000162591	3_prime_UTR_variant	ENSG00000162591	6,273	ENSG00000162591	3,042	3,042	ENSG00000162591	3_prime_UTR_variant	NA	NA
1	3,499,885	C	A	false	missense_variant	88	rs7553399	0.000238		0.26391	51.224	missense_variant	missense_variant	ENSG00000162591	0	ENSG00000162591	0	0	ENSG00000162591	missense_variant	ENSG00000162591	3,167	ENSG00000162591	3,870	3,167	ENSG00000162591	missense_variant	NA	NA
1	3,505,022	C	T	false	distal	6	rs6669870	0.000432		0.13902	35.291	intron_variant	dELS_flank	ENSG00000162591	185	ENSG00000162591	185	185	ENSG00000162591	dELS_flank	ENSG00000162591	8,304	ENSG00000162591	9,007	8,304	ENSG00000162591	distal	NA	NA
1	3,517,003	C	T	false	distal	49	rs2820997	0.009617		0.10059	79.721	intron_variant	dELS	ENSG00000162591	1,475	ENSG00000162591	1,475	1,475	ENSG00000162591	dELS	ENSG00000162591	14,419	ENSG00000162591	20,988	14,419	ENSG00000162591	distal	NA	NA
1	3,622,917	A	G	false	non_coding_transcript_exon_variant	120	rs10909990	0.003065		0.221	47.938	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000158109	2,097	ENSG00000238260	0	0	ENSG00000238260	non_coding_transcript_exon_variant	ENSG00000158109	2,097	ENSG00000238260	1,832	1,832	ENSG00000238260	non_coding_transcript_exon_variant	NA	NA
1	3,752,608	C	T	false	missense_variant	108	rs41315312	0.000043		0.06798	31.321	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000162592	157	ENSG00000162592	162	157	ENSG00000162592	missense_variant	NA	NA
1	3,752,641	C	G	false	missense_variant	74	rs10910021	0.004863		0.34899	53.928	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000162592	190	ENSG00000162592	195	190	ENSG00000162592	missense_variant	NA	NA
1	3,752,792	G	A	false	missense_variant	102	rs76597070	0.000377		0.012182	8.5963	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000162592	341	ENSG00000162592	346	341	ENSG00000162592	missense_variant	NA	NA
1	3,762,639	C	T	false	missense_variant	77	rs75571263	0.000057		0.000046	10.277	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000235169	10,109	ENSG00000162592	10,193	10,109	ENSG00000235169	missense_variant	NA	NA
1	3,763,219	T	C	false	missense_variant	75	rs76416341	0.000263		0.006047	8.699	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000235169	9,529	ENSG00000162592	10,773	9,529	ENSG00000235169	missense_variant	NA	NA
1	3,763,322	C	T	false	missense_variant	77	rs11806371	0.000046		0.001043	19.395	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000235169	9,426	ENSG00000162592	10,876	9,426	ENSG00000235169	missense_variant	NA	NA
1	3,763,781	C	T	false	missense_variant	75	rs144028564	0.000088		0.005643	2.4453	missense_variant	missense_variant	ENSG00000162592	0	ENSG00000162592	0	0	ENSG00000162592	missense_variant	ENSG00000235169	8,967	ENSG00000162592	11,335	8,967	ENSG00000235169	missense_variant	NA	NA
1	3,772,844	G	A	false	splicing	168	rs2275819	0.000477		0.074456	59.967	splice_donor_region_variant	splice_donor_region_variant	ENSG00000235169	0	ENSG00000162592	1,198	0	ENSG00000235169	splice_donor_region_variant	ENSG00000235169	18	ENSG00000266075	9,970	18	ENSG00000235169	splicing	NA	splicing:b0
1	3,774,964	A	G	true	distal	28	rs1175550	0.999975	Hb,HbA1c,MCHC,RBC	0.23057	95.317	intron_variant	dELS	ENSG00000235169	334	ENSG00000162592	3,318	334	ENSG00000235169	dELS	ENSG00000235169	2,138	ENSG00000266075	7,850	2,138	ENSG00000235169	distal	NA	NA
1	3,787,025	C	T	false	missense_variant	78	rs138729139	0.000128		0.006097	5.7844	missense_variant	missense_variant	ENSG00000130764	0	ENSG00000272153	1,486	0	ENSG00000130764	missense_variant	ENSG00000130764	9,472	ENSG00000272153	2,016	2,016	ENSG00000272153	missense_variant	NA	NA
1	3,796,513	G	T	false	tss_proximal	173	rs12759775	0.003388		0.10405	80.252	upstream_gene_variant	PLS	ENSG00000130764	14	ENSG00000272153	10,974	14	ENSG00000130764	tss_proximal	ENSG00000130764	14	ENSG00000272153	11,504	14	ENSG00000130764	tss_proximal	tss_prox:b0	tss_prox:b0
1	3,871,185	C	G	false	distal	43	rs6670527	0.000147		0.39234	44.304	intron_variant	dELS	ENSG00000169598	1,286	ENSG00000169598	1,286	1,286	ENSG00000169598	dELS	ENSG00000169598	13,708	ENSG00000169598	3,521	3,521	ENSG00000169598	distal	NA	NA
1	3,964,554	A	G	false	distal	161	rs10799215	0.000151		0.36669	75.296	intergenic_variant	intergenic_variant	ENSG00000198912	64,281	ENSG00000233304	9,291	9,291	ENSG00000233304	intergenic_variant	ENSG00000198912	64,281	ENSG00000284668	11,578	11,578	ENSG00000284668	distal	NA	NA
1	3,965,882	C	T	false	distal	161	rs7550426	0.000186		0.36067	74.807	intergenic_variant	intergenic_variant	ENSG00000198912	65,609	ENSG00000284668	10,250	10,250	ENSG00000284668	intergenic_variant	ENSG00000198912	65,609	ENSG00000284668	10,250	10,250	ENSG00000284668	distal	NA	NA
1	3,966,008	G	A	false	distal	161	rs12031275	0.00016		0.36661	75.318	intergenic_variant	intergenic_variant	ENSG00000198912	65,735	ENSG00000284668	10,124	10,124	ENSG00000284668	intergenic_variant	ENSG00000198912	65,735	ENSG00000284668	10,124	10,124	ENSG00000284668	distal	NA	NA
1	3,966,261	A	C	false	distal	161	rs10915483	0.000192		0.36372	74.883	intergenic_variant	intergenic_variant	ENSG00000198912	65,988	ENSG00000284668	9,871	9,871	ENSG00000284668	intergenic_variant	ENSG00000198912	65,988	ENSG00000284668	9,871	9,871	ENSG00000284668	distal	NA	NA
1	3,966,301	G	C	false	distal	161	rs10915484	0.000162		0.36659	75.321	intergenic_variant	intergenic_variant	ENSG00000198912	66,028	ENSG00000284668	9,831	9,831	ENSG00000284668	intergenic_variant	ENSG00000198912	66,028	ENSG00000284668	9,831	9,831	ENSG00000284668	distal	NA	NA
1	5,905,395	C	T	false	missense_variant	109	rs571655	0.000012		0.012417	16.232	missense_variant	missense_variant	ENSG00000131697	0	ENSG00000131697	0	0	ENSG00000131697	missense_variant	ENSG00000069424	85,531	ENSG00000131697	70	70	ENSG00000131697	missense_variant	NA	NA
1	5,905,434	C	T	false	missense_variant	109	rs201282741	0.000014		0.000419	2.7215	missense_variant	missense_variant	ENSG00000131697	0	ENSG00000131697	0	0	ENSG00000131697	missense_variant	ENSG00000069424	85,492	ENSG00000131697	109	109	ENSG00000131697	missense_variant	NA	NA
1	5,905,764	G	C	false	missense_variant	109	rs12093500	0.000008		0.001044	99.802	missense_variant	missense_variant	ENSG00000131697	0	ENSG00000131697	0	0	ENSG00000131697	missense_variant	ENSG00000069424	85,162	ENSG00000131697	439	439	ENSG00000131697	missense_variant	NA	NA
1	5,963,761	C	T	false	distal	171	rs7515065	0.000013		0.36005	152.05	intron_variant	CA-CTCF_flank	ENSG00000131697	1,811	ENSG00000131697	1,811	1,811	ENSG00000131697	CA-CTCF_flank	ENSG00000069424	27,165	ENSG00000131697	28,662	27,165	ENSG00000069424	distal	NA	NA
1	5,963,780	C	T	false	distal	171	rs7515070	0.000013		0.36005	152.05	intron_variant	CA-CTCF_flank	ENSG00000131697	1,830	ENSG00000131697	1,830	1,830	ENSG00000131697	CA-CTCF_flank	ENSG00000069424	27,146	ENSG00000131697	28,643	27,146	ENSG00000069424	distal	NA	NA
1	5,964,813	A	G	false	distal	171	rs2047810	0.000011		0.35892	152.11	intron_variant	CA-CTCF_flank	ENSG00000131697	2,485	ENSG00000131697	2,485	2,485	ENSG00000131697	CA-CTCF_flank	ENSG00000069424	26,113	ENSG00000131697	27,610	26,113	ENSG00000069424	distal	NA	NA
1	5,967,533	G	A	false	distal	37	rs75504751	0.000029		0.070407	34.201	intron_variant	dELS	ENSG00000131697	169	ENSG00000131697	169	169	ENSG00000131697	dELS	ENSG00000069424	23,393	ENSG00000131697	24,890	23,393	ENSG00000069424	distal	NA	NA
1	5,968,552	T	C	false	distal	37	rs553959	0.000053		0.06477	56.394	intron_variant	dELS	ENSG00000131697	534	ENSG00000131697	534	534	ENSG00000131697	dELS	ENSG00000069424	22,374	ENSG00000131697	23,871	22,374	ENSG00000069424	distal	NA	NA
1	5,995,424	G	A	false	distal	40	rs111391080	0.000056		0.02269	23.621	intron_variant	dELS	ENSG00000069424	438	ENSG00000069424	438	438	ENSG00000069424	dELS	ENSG00000069424	2,663	ENSG00000069424	2,692	2,663	ENSG00000069424	distal	NA	NA
1	5,999,073	G	A	false	distal	28	rs11120998	0.000051		0.23491	87.161	intron_variant	dELS	ENSG00000069424	2,988	ENSG00000069424	2,988	2,988	ENSG00000069424	dELS	ENSG00000069424	6,312	ENSG00000069424	6,341	6,312	ENSG00000069424	distal	NA	NA
1	6,027,351	T	C	false	splicing	184	rs1296422	0.000019		0.04745	46.688	splice_region_variant	splice_region_variant	ENSG00000069424	0	ENSG00000069424	905	0	ENSG00000069424	splice_region_variant	ENSG00000069424	53	ENSG00000069424	1,005	53	ENSG00000069424	splicing	NA	splicing:b0
1	6,035,020	C	T	false	5_prime_UTR_variant	127	rs115247000	0.000007		0.008918	32.008	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000069424	0	ENSG00000069424	896	0	ENSG00000069424	5_prime_UTR_variant	ENSG00000069424	39	ENSG00000069424	896	39	ENSG00000069424	5_prime_UTR_variant	NA	NA
1	6,153,103	G	T	false	distal	36	rs6679857	0.000017		0.20087	74.559	intron_variant	dELS	ENSG00000116254	566	ENSG00000116254	566	566	ENSG00000116254	dELS	ENSG00000116254	27,217	ENSG00000116254	8,998	8,998	ENSG00000116254	distal	NA	NA
1	6,168,838	A	G	false	distal	24	rs11808801	0.00003		0.094174	84.556	intron_variant	dELS_flank	ENSG00000116254	560	ENSG00000285629	560	560	ENSG00000116254	dELS_flank	ENSG00000116254	11,482	ENSG00000116254	11,184	11,184	ENSG00000116254	distal	NA	NA
1	6,206,584	G	A	false	missense_variant	110	rs142728754	0.000023		0.000984	4.6555	missense_variant	missense_variant	ENSG00000158286	0	ENSG00000158286	0	0	ENSG00000158286	missense_variant	ENSG00000158286	464	ENSG00000158286	454	454	ENSG00000158286	missense_variant	NA	NA
1	6,254,762	T	C	false	synonymous_variant	187	rs11590458	0.00025		0.30907	65.607	synonymous_variant	synonymous_variant	ENSG00000158292	0	ENSG00000097021	9,510	0	ENSG00000158292	synonymous_variant	ENSG00000158292	6,335	ENSG00000225077	16,990	6,335	ENSG00000158292	synonymous_variant	NA	NA
1	6,393,563	C	T	false	5_prime_UTR_variant	129	rs56933792	0.000508		0.073672	156.56	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000097021	0	ENSG00000271746	0	0	ENSG00000097021	5_prime_UTR_variant	ENSG00000097021	201	ENSG00000271746	7	7	ENSG00000271746	5_prime_UTR_variant	NA	NA
1	6,393,684	C	A	false	5_prime_UTR_variant	129	rs58125749	0.000536		0.07369	156.58	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000097021	0	ENSG00000271746	0	0	ENSG00000097021	5_prime_UTR_variant	ENSG00000097021	81	ENSG00000271746	128	81	ENSG00000097021	5_prime_UTR_variant	NA	NA
1	6,408,110	T	C	false	distal	42	rs60789020	0.000232		0.19134	233.59	intergenic_variant	dELS	ENSG00000069812	4,307	ENSG00000069812	4,939	4,307	ENSG00000069812	dELS	ENSG00000069812	11,792	ENSG00000069812	8,520	8,520	ENSG00000069812	distal	NA	NA
1	6,425,727	G	T	false	tss_proximal	141	rs61780701	0.00007		0.037704	157.96	intron_variant	pELS	ENSG00000187017	477	ENSG00000265392	4,106	477	ENSG00000187017	tss_proximal	ENSG00000187017	938	ENSG00000265392	4,168	938	ENSG00000187017	tss_proximal	tss_prox:b1	tss_prox:b1
1	6,447,876	G	C	false	tss_proximal	140	rs115330145	0.000067		0.059695	119.7	intron_variant	PLS	ENSG00000187017	166	ENSG00000231868	869	166	ENSG00000187017	tss_proximal	ENSG00000187017	166	ENSG00000231868	869	166	ENSG00000187017	tss_proximal	tss_prox:b1	tss_prox:b1

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evals_complex_traits

Variant-effect-prediction benchmark of UKBB fine-mapped complex-trait SNVs vs low-PIP SNVs, 1:9 matched within consequence categories on (chrom, consequence_final) plus subset-targeted distance bins, with MAF entering as a continuous matching feature.

Description


Positives	UKBB SuSiE+FINEMAP fine-mapped variants with max(PIP) > 0.9 across 119 traits
Negatives	max(PIP) < 0.01 across 119 traits, 1:9 matched per positive
Genome build	GRCh38 (lifted from hg19)
Variant type	SNVs only
Coordinates	1-based (`pos` is 1-based; `ref`/`alt` are single bases)
Matching ratio	1:9

Splits

Split	Variants (pos + 9·neg)	Positives	Chromosomes
`train`	11,630	1,163	odd: 1, 3, …, X
`test`	10,000	1,000	even: 2, 4, …, Y
total	21,630	2,163

Columns

Column	Type	Description
`chrom`, `pos`, `ref`, `alt`	str / int / str / str	Variant coordinates (1-based, GRCh38)
`label`	bool	`True` for high-PIP positive, `False` for low-PIP matched negative
`subset`	str	Consequence-group label for stratified eval
`match_group`	int	Integer ID grouping each positive with its 9 matched negatives
`rsid`	str	dbSNP rsID (when available)
`pip`	float	Maximum PIP across the 119 traits
`traits`	str	Comma-separated list of traits with PIP > 0.9 (positives only)
`MAF`	float	UKBB EUR minor allele frequency
`ld_score`	float	UKBB EUR LD score (passthrough, not a matching feature)
`consequence`, `consequence_cre`, `consequence_final`, `consequence_group`	str	Ensembl VEP consequence + grouping
`distance_tss_pc`, `distance_tss_nc`, `distance_tss`	int	Distances to nearest protein-coding / non-protein-coding TSS (and min, used for `consequence_group` recategorization)
`tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `tss_closest_gene_id`	str	Ensembl gene IDs (passthrough — gene-id was not used in matching)
`distance_exon_pc`, `distance_exon_nc`, `distance_exon`	int	Same shape, for nearest exon
`exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`, `exon_closest_gene_id`	str	Same shape
`distance_tss_pc_bin`, `distance_exon_pc_bin`	str	Subset-prefixed bin labels used as exact-match keys; `BIN_NA` outside the binned subsets

Per-subset retention

Subset	n_pos in `dataset_all`	matched (kept)	retention
`distal`	1,193	1,193	100.0%
`missense_variant`	454	454	100.0%
`tss_proximal`	244	244	100.0%
`3_prime_UTR_variant`	78	78	100.0%
`non_coding_transcript_exon_variant`	75	75	100.0%
`5_prime_UTR_variant`	56	56	100.0%
`synonymous_variant`	33	33	100.0%
`splicing`	30	30	100.0%
`mature_miRNA_variant`	2	0	0.0%
total	2,165	2,163	99.9%

Matching design

Matching is exact on every categorical key, then Euclidean-nearest on the (RobustScaler-scaled) continuous features as a within-group tie-breaker. Without replacement, k=9.

Continuous features: distance_tss_pc, distance_tss_nc, distance_exon_pc, distance_exon_nc, MAF.
Categorical features:
- chrom, consequence_final
- distance_tss_pc_bin — tss_proximal: edges [0, 100, 1000, ∞]; BIN_NA elsewhere
- distance_exon_pc_bin —
  - tss_proximal: edges [0, 100, 1000, ∞]
  - splicing: edges [0, 5, 30, ∞]
  - BIN_NA elsewhere

Gene-ID columns are kept as passthrough metadata but not used as match keys.

Matched-feature AUPRC diagnostic

Each continuous matching feature f is scored as a single-feature predictor within each subset: {f}_auprc = max(AP(label, +f), AP(label, −f)). Baseline = 0.1 for 1:9 matching.

Per-(subset, feature) AUPRC table

subset	n	distance_tss_pc	distance_tss_nc	distance_exon_pc	distance_exon_nc	MAF
`distal`	1,193	0.101	0.102	0.109	0.105	0.101
`missense_variant`	454	0.108	0.106	0.102	0.104	0.108
`tss_proximal`	244	0.114	0.114	0.110	0.108	0.101
`3_prime_UTR_variant`	78	0.119	0.116	0.108	0.108	0.114
`non_coding_transcript_exon_variant`	75	0.110	0.112	0.124	0.100	0.106
`5_prime_UTR_variant`	56	0.123	0.109	0.102	0.110	0.109
`synonymous_variant`	33	0.120	0.106	0.107	0.111	0.107
`splicing`	30	0.124	0.131	0.108	0.131	0.122

Provenance

Built by the bolinas-dna eval pipeline at commit main.

Curation pipeline: snakemake/evals
Matching algorithm: src/bolinas/pipelines/evals/matching.py
Diagnostic helper: src/bolinas/pipelines/evals/matching_qc.py

The curation is a from-scratch reimplementation of the TraitGym complex-traits pipeline.

License

Released under the same terms as its sources. UKBB summary-level data and the Finucane lab fine-mapping release are intended for non-commercial research; check upstream license if you plan to use commercially.

Citation

TraitGym — Benegas et al. 2025, bioRxiv 2025.02.11.637758
UKBB fine-mapping — Wang et al. (Nat Commun 2021) and the Finucane lab release
LD scores — Bulik-Sullivan et al. (Nat Genet 2015)

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