Variant report

Variant	rs7652172
Chromosome Location	chr3:119764086-119764087
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	chr3:119763698..119765410-chr3:119769274..119771635,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10433404	0.85[YRI][hapmap]
rs10934500	0.82[YRI][hapmap]
rs10934502	0.85[YRI][hapmap]
rs10934503	0.84[YRI][hapmap]
rs10934505	0.85[YRI][hapmap]
rs10934506	0.85[YRI][hapmap]
rs10934507	0.91[YRI][hapmap]
rs1154596	1.00[CHB][hapmap]
rs1154597	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11915717	0.85[YRI][hapmap]
rs11921053	0.91[EUR][1000 genomes]
rs12494560	0.81[AMR][1000 genomes]
rs12629015	0.85[YRI][hapmap]
rs12634476	0.85[YRI][hapmap]
rs12638973	0.84[YRI][hapmap]
rs13312998	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13314595	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];0.97[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1574154	0.85[YRI][hapmap]
rs1579031	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16830683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs16830689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719887	1.00[CHB][hapmap]
rs1719888	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs1719889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1719895	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1732170	0.82[CEU][hapmap]
rs182839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs184576	0.82[ASN][1000 genomes]
rs1870931	0.85[YRI][hapmap]
rs28516957	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108749	1.00[CHB][hapmap]
rs334533	0.82[CEU][hapmap]
rs334534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs334535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334552	0.84[ASN][1000 genomes]
rs334554	0.84[ASN][1000 genomes]
rs334559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334560	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334561	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072520	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4340737	0.85[YRI][hapmap]
rs4450859	0.85[AMR][1000 genomes]
rs4624596	0.85[YRI][hapmap]
rs4688042	0.85[YRI][hapmap]
rs4688043	1.00[CHB][hapmap]
rs4688046	0.85[YRI][hapmap]
rs4688047	0.85[YRI][hapmap]
rs4688054	0.85[YRI][hapmap]
rs56126162	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58043853	0.91[EUR][1000 genomes]
rs6438554	1.00[CHB][hapmap]
rs6438555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650215	0.82[EUR][1000 genomes]
rs6769435	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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6774693	0.98[EUR][1000 genomes]
rs6775397	0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6779828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784239	1.00[CHB][hapmap]
rs6785050	1.00[CHB][hapmap]
rs6790751	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6795874	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs6802301	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805931	0.84[ASN][1000 genomes]
rs6807868	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7613197	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7620750	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7624540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs7628426	0.84[ASN][1000 genomes]
rs7633279	0.85[YRI][hapmap]
rs7636600	0.93[EUR][1000 genomes]
rs7644234	0.82[CEU][hapmap]
rs7649661	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs9289138	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs9851174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119751800-119766800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:119757000-119765000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr3:119757200-119765800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:119757800-119769800	ZNF genes & repeats	Dnd41	blood
5	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
6	chr3:119760000-119764200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:119760000-119770200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:119760000-119771200	Weak transcription	NHDF-Ad	bronchial
9	chr3:119760200-119764200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:119760200-119764200	Weak transcription	Aorta	Aorta
11	chr3:119760200-119766400	Weak transcription	Colonic Mucosa	Colon
12	chr3:119760200-119767400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:119760200-119767400	Weak transcription	Right Ventricle	heart
14	chr3:119760200-119768200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:119760200-119768600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:119760200-119768800	Weak transcription	Ovary	ovary
17	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:119760200-119805400	Weak transcription	HMEC	breast
19	chr3:119760400-119764400	Weak transcription	HepG2	liver
20	chr3:119760800-119767400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:119761200-119769200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:119761400-119765400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:119761400-119768000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:119761600-119768200	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:119762200-119764800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
26	chr3:119762200-119765000	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr3:119762400-119764600	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr3:119762400-119764800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:119762800-119764600	ZNF genes & repeats	Fetal Thymus	thymus
30	chr3:119762800-119765000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:119763000-119764800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr3:119763000-119765000	ZNF genes & repeats	GM12878-XiMat	blood
33	chr3:119763200-119764200	Weak transcription	Brain Substantia Nigra	brain
34	chr3:119763200-119764200	Weak transcription	Thymus	Thymus
35	chr3:119763200-119764400	Weak transcription	Pancreas	Pancrea
36	chr3:119763200-119765000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:119763200-119769600	Weak transcription	Gastric	stomach
38	chr3:119763400-119766800	Weak transcription	Brain Angular Gyrus	brain
39	chr3:119763600-119764400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:119763800-119764800	ZNF genes & repeats	Fetal Lung	lung
41	chr3:119764000-119764800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:119764000-119765200	ZNF genes & repeats	NHEK	skin

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