Variant report

Variant	rs940966
Chromosome Location	chr15:52691967-52691968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52691750..52693545-chr15:52696504..52698685,2	MCF-7	breast:
2	chr15:52684122..52687406-chr15:52689742..52694048,4	MCF-7	breast:

Extended variants
information (count: 165 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1001407	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10518684	1.00[CHB][hapmap]
rs10518689	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10518691	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10518692	1.00[CHB][hapmap]
rs1058219	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10851514	0.81[EUR][1000 genomes]
rs10851515	0.81[EUR][1000 genomes]
rs10851516	0.81[EUR][1000 genomes]
rs10851517	0.81[EUR][1000 genomes]
rs11631183	0.85[ASN][1000 genomes]
rs11852261	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11852555	0.81[EUR][1000 genomes]
rs11853078	0.90[JPT][hapmap]
rs11853114	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11853179	0.93[CHB][hapmap];0.94[TSI][hapmap]
rs11853337	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11853455	0.81[EUR][1000 genomes]
rs11853586	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11853802	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11853875	0.81[EUR][1000 genomes]
rs11853954	0.82[TSI][hapmap]
rs11854130	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs11854247	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs11854456	0.81[EUR][1000 genomes]
rs11854498	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11854673	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs11854780	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11854886	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11855082	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap]
rs11855252	0.81[EUR][1000 genomes]
rs11855257	0.80[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11855295	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11855453	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs11855584	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11855640	0.80[ASN][1000 genomes]
rs11855820	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11855884	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11856588	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11856662	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11856752	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11856810	0.93[CEU][hapmap];0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs11856896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11857993	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11858031	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11858927	0.81[EUR][1000 genomes]
rs1464965	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs1464966	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs1474435	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1474436	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1474437	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1474438	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1693492	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs1693494	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes]
rs1693497	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs1693501	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs1693502	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs1693506	0.93[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1693507	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs1693508	0.81[CEU][hapmap]
rs1724578	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1724579	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1724588	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1724590	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1724595	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs1724601	0.81[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs1724603	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1724608	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1724616	0.81[AMR][1000 genomes]
rs1724637	0.81[AMR][1000 genomes]
rs1724638	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17541809	0.96[EUR][1000 genomes]
rs17613587	0.92[EUR][1000 genomes]
rs17613607	0.92[EUR][1000 genomes]
rs17613951	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17651212	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17651218	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17651230	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17651242	0.86[EUR][1000 genomes]
rs17651326	1.00[CHB][hapmap]
rs17651397	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17651611	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17651631	0.93[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs17707338	0.92[EUR][1000 genomes]
rs17707651	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17707705	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17707729	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17707996	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs17708103	0.93[CHB][hapmap]
rs1815176	0.85[EUR][1000 genomes]
rs1869126	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1869127	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs1869128	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2140962	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2177876	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2257152	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2272283	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs2290334	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[EUR][1000 genomes]
rs2414148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414152	0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs2462857	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2693462	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs2693466	0.81[AMR][1000 genomes]
rs28422901	0.81[AMR][1000 genomes]
rs28680872	0.80[EUR][1000 genomes]
rs2899488	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs35943650	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36074938	0.81[EUR][1000 genomes]
rs3751619	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs3751620	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3794568	0.96[EUR][1000 genomes]
rs3816449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs41408650	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs4341694	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs4774622	0.84[ASN][1000 genomes]
rs4774623	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774624	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs4774625	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4774627	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap]
rs4776044	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776045	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4776051	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap]
rs4776053	0.93[CEU][hapmap];0.93[CHB][hapmap];0.97[TSI][hapmap]
rs55706220	0.81[EUR][1000 genomes]
rs55722736	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55978431	0.96[EUR][1000 genomes]
rs56039749	0.81[EUR][1000 genomes]
rs56128753	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56136255	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56148029	0.81[EUR][1000 genomes]
rs56227135	0.81[EUR][1000 genomes]
rs56315558	0.81[EUR][1000 genomes]
rs56360952	0.81[EUR][1000 genomes]
rs56749732	0.81[EUR][1000 genomes]
rs56850880	0.81[EUR][1000 genomes]
rs56992654	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58043289	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59496859	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59584964	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60248452	0.81[EUR][1000 genomes]
rs60512163	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493561	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs67283829	0.81[EUR][1000 genomes]
rs67399033	0.81[EUR][1000 genomes]
rs68101123	0.81[EUR][1000 genomes]
rs68155341	0.96[EUR][1000 genomes]
rs7162731	0.81[MEX][hapmap]
rs7165578	0.81[MEX][hapmap]
rs7178839	0.80[ASN][1000 genomes]
rs72623980	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72736633	0.85[ASN][1000 genomes]
rs72736668	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72736669	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72736696	0.81[EUR][1000 genomes]
rs8030731	0.81[AMR][1000 genomes]
rs940967	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940968	0.83[AMR][1000 genomes]
rs940971	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs940972	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs940973	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs9788691	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs940966	POP1	trans	cerebellum	SCAN
rs940966	KIAA1370	Cis_1M	lymphoblastoid	RTeQTL
rs940966	MYO5A	cis	multi-tissue	Pritchard
rs940966	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs940966	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs940966	MYO5A	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
5	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
6	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
9	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
11	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:52676200-52701800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:52676400-52696800	Weak transcription	Brain Germinal Matrix	brain
14	chr15:52676400-52696800	Weak transcription	Dnd41	blood
15	chr15:52676400-52697000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:52676400-52699600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:52676400-52701000	Weak transcription	HMEC	breast
18	chr15:52676400-52709800	Weak transcription	NHLF	lung
19	chr15:52676400-52721400	Weak transcription	Gastric	stomach
20	chr15:52676600-52698000	Weak transcription	Fetal Thymus	thymus
21	chr15:52676600-52701800	Weak transcription	Right Ventricle	heart
22	chr15:52676600-52706400	Weak transcription	Lung	lung
23	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
27	chr15:52680600-52719800	Weak transcription	NH-A	brain
28	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
30	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
31	chr15:52681000-52696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:52681000-52696800	Weak transcription	Ovary	ovary
33	chr15:52681000-52706800	Weak transcription	Brain Substantia Nigra	brain
34	chr15:52681200-52701000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:52682600-52693200	Strong transcription	Primary B cells from cord blood	blood
36	chr15:52683800-52696800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:52684000-52693600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:52684400-52696600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:52684400-52696800	Weak transcription	HSMM	muscle
41	chr15:52684600-52695400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:52684800-52695600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:52684800-52701000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:52685000-52696800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:52685000-52701200	Weak transcription	A549	lung
48	chr15:52685000-52717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:52685200-52696800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:52685200-52701000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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