Variant report

Variant	rs7976058
Chromosome Location	chr12:62675647-62675648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:62675578-62675940	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62653360..62655932-chr12:62673636..62676374,2	MCF-7	breast:
2	chr12:62674932..62676945-chr12:62683042..62684862,2	K562	blood:

Variant related genes	Relation type
FAM19A2	TF binding region
ENSG00000198673	Chromatin interaction
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10160868	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs10160955	0.82[CHD][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs10431509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459253	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10506440	0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10747958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784292	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10877819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10877820	0.97[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10877824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877826	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10877829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877831	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877834	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs11174397	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11174398	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs11174399	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs11174401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174404	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174408	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174409	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11174410	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11174411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174412	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174416	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174417	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174418	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11174420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174423	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174424	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174431	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11174433	0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174435	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174436	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11174437	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11174438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11174449	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11174458	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs11504121	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11504122	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11561463	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836268	0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12228015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12229271	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12231778	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297474	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12297480	0.80[AFR][1000 genomes]
rs12299072	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12306066	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12307900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308455	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12310318	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12310616	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310651	0.82[CHD][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12311259	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12311279	0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12315645	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12317437	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12318287	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12424732	0.86[MKK][hapmap]
rs1376342	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1496859	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1901239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131435	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2132651	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2167287	0.80[CHD][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs2242032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28526400	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35634758	0.87[ASN][1000 genomes]
rs3803106	0.82[CHD][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6581444	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66507062	0.82[AFR][1000 genomes]
rs67044039	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67853252	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7132814	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133294	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137068	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295013	0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7298827	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7300928	0.87[ASW][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7302033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302617	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73136889	0.80[AFR][1000 genomes]
rs73321563	0.87[AFR][1000 genomes]
rs767391	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs7953967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956332	0.87[AFR][1000 genomes]
rs7963950	0.82[CHD][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7965326	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971588	0.82[AFR][1000 genomes]
rs7974973	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7976608	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs902971	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9634284	0.96[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62655400-62685600	Weak transcription	HSMM	muscle
2	chr12:62656400-62679400	Weak transcription	Brain Anterior Caudate	brain
3	chr12:62656600-62685600	Weak transcription	Aorta	Aorta
4	chr12:62656600-62685600	Weak transcription	Pancreas	Pancrea
5	chr12:62661600-62676000	Weak transcription	Fetal Thymus	thymus
6	chr12:62661600-62682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:62662200-62676000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:62663000-62685600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:62663200-62684800	Weak transcription	NHEK	skin
10	chr12:62663400-62685600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:62664400-62685400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:62664800-62676200	Weak transcription	Hela-S3	cervix
13	chr12:62665000-62688000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:62665800-62679000	Weak transcription	Fetal Lung	lung
15	chr12:62666800-62678200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:62666800-62681600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:62667200-62677000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:62667200-62682200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:62667800-62676400	Weak transcription	A549	lung
20	chr12:62667800-62689000	Weak transcription	HSMMtube	muscle
21	chr12:62668400-62679200	Weak transcription	Fetal Brain Male	brain
22	chr12:62668400-62682000	Weak transcription	NHLF	lung
23	chr12:62668800-62678000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:62669200-62677200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr12:62669600-62680400	Weak transcription	Right Ventricle	heart
26	chr12:62669800-62675800	Weak transcription	Ovary	ovary
27	chr12:62669800-62675800	Weak transcription	Right Atrium	heart
28	chr12:62669800-62676200	Weak transcription	Adipose Nuclei	Adipose
29	chr12:62669800-62679200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:62669800-62688400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:62670000-62679200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:62670000-62688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:62670800-62679200	Weak transcription	NHDF-Ad	bronchial
34	chr12:62671200-62676200	Weak transcription	Fetal Heart	heart
35	chr12:62671400-62675800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:62671400-62680000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:62672800-62677400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:62672800-62678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:62673200-62677800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:62673400-62678600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:62673600-62677400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr12:62673800-62675800	Weak transcription	Liver	Liver
43	chr12:62674200-62676000	Enhancers	Primary B cells from peripheral blood	blood
44	chr12:62674200-62677400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:62674200-62680400	Weak transcription	Fetal Intestine Small	intestine
46	chr12:62674200-62685400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:62674400-62676400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:62674400-62676600	Enhancers	Dnd41	blood
49	chr12:62674400-62685600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:62674600-62675800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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