Variant report

Variant	rs7309659
Chromosome Location	chr12:57739634-57739635
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	chr12:57735230..57737422-chr12:57738805..57741589,2	K562	blood:
2	chr12:57734900..57736730-chr12:57737595..57740305,2	K562	blood:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783818	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783820	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876976	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876977	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876978	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876981	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172160	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172165	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172169	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172177	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172190	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs11172191	0.81[EUR][1000 genomes]
rs11609986	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs12230111	0.86[ASN][1000 genomes]
rs12296766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310220	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12579911	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1798710	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2063778	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2280139	0.80[JPT][hapmap]
rs28504983	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35032945	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923885	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs4075325	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4108243	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4760192	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760193	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760228	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760236	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760305	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760306	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.87[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760348	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760357	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481196	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs491750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs492749	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs512223	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533975	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs537482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs543410	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs560048	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs568793	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs575153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6581134	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581135	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581136	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581139	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133366	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7133939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7135142	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7298418	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303070	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307059	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313824	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314266	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7358684	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7398058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486863	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7975649	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7977908	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7980310	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7309659	SPRY2	trans	lymphoblastoid	seeQTL
rs7309659	OR6C4	cis	parietal	SCAN
rs7309659	DKFZP586D0919	cis	multi-tissue	Pritchard
rs7309659	KRT85	cis	parietal	SCAN
rs7309659	XRCC6BP1	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57693600-57743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:57694000-57780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:57695200-57794600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:57697200-57745000	Weak transcription	Lung	lung
5	chr12:57699800-57762400	Weak transcription	Left Ventricle	heart
6	chr12:57703400-57742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:57704200-57743200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:57704400-57789200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:57709800-57746800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:57713800-57745800	Weak transcription	Stomach Mucosa	stomach
11	chr12:57722000-57741000	Weak transcription	Dnd41	blood
12	chr12:57722000-57765200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:57722200-57743600	Weak transcription	Aorta	Aorta
14	chr12:57722600-57744200	Weak transcription	Fetal Intestine Large	intestine
15	chr12:57722800-57741000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:57722800-57771200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:57722800-57786200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:57725800-57743200	Weak transcription	Placenta	Placenta
19	chr12:57726000-57759800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:57726200-57741400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:57726600-57754200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:57727200-57745000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:57727200-57748200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:57727200-57764400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:57728000-57743800	Weak transcription	NHEK	skin
26	chr12:57728000-57766600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:57728800-57746600	Weak transcription	Gastric	stomach
28	chr12:57731400-57789800	Weak transcription	Small Intestine	intestine
29	chr12:57731600-57796000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:57732800-57771800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:57733200-57744200	Weak transcription	Liver	Liver
32	chr12:57733400-57741200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:57733400-57742000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:57733600-57745000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:57733600-57762400	Weak transcription	Thymus	Thymus
36	chr12:57734200-57779400	Weak transcription	Spleen	Spleen
37	chr12:57734400-57741000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:57734400-57741200	Weak transcription	Adipose Nuclei	Adipose
39	chr12:57734400-57742400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:57734400-57748400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:57734400-57760000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:57734600-57740800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:57735000-57741200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:57735200-57764400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:57735400-57749200	Weak transcription	Psoas Muscle	Psoas
46	chr12:57735600-57740800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:57735600-57750000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:57736400-57740600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:57736400-57740600	Weak transcription	Fetal Thymus	thymus
50	chr12:57736400-57740800	Weak transcription	Osteobl	bone

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