Variant report

Variant	rs7646541
Chromosome Location	chr3:23534073-23534074
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23533666..23536566-chr3:23556700..23559047,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10510539	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11129120	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11713090	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11715736	0.86[EUR][1000 genomes]
rs11718111	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs13316118	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs13323077	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1391756	0.85[EUR][1000 genomes]
rs1498810	0.87[EUR][1000 genomes]
rs1498812	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1692621	0.85[CEU][hapmap]
rs1692646	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1692647	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692648	0.86[EUR][1000 genomes]
rs1692649	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1695180	0.81[CEU][hapmap]
rs1695183	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1695185	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1695192	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1695197	0.84[EUR][1000 genomes]
rs1695203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17013268	0.81[CEU][hapmap]
rs17013425	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17194751	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs1874502	0.80[CEU][hapmap]
rs1874503	0.81[CEU][hapmap]
rs1995173	0.86[EUR][1000 genomes]
rs1995174	0.87[EUR][1000 genomes]
rs1995175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036044	0.81[CEU][hapmap]
rs2055155	0.95[CEU][hapmap]
rs2055307	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs56034809	0.86[EUR][1000 genomes]
rs58130044	0.85[EUR][1000 genomes]
rs58718028	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59012069	0.87[EUR][1000 genomes]
rs62255784	0.88[EUR][1000 genomes]
rs62255785	0.87[EUR][1000 genomes]
rs62255789	0.86[EUR][1000 genomes]
rs62256989	0.87[ASN][1000 genomes]
rs6550754	0.90[CEU][hapmap]
rs6780388	0.81[CEU][hapmap]
rs6801824	0.81[CEU][hapmap]
rs6807859	0.87[EUR][1000 genomes]
rs73139773	0.87[EUR][1000 genomes]
rs73140544	0.86[EUR][1000 genomes]
rs7431560	0.93[ASN][1000 genomes]
rs7614195	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7629327	0.95[CEU][hapmap]
rs7636705	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7643705	0.81[CEU][hapmap]
rs7648425	0.95[CEU][hapmap]
rs778465	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs778479	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778483	0.85[CEU][hapmap]
rs778489	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs778491	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778492	0.80[CEU][hapmap]
rs778493	0.88[JPT][hapmap]
rs778502	0.85[CEU][hapmap]
rs778511	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs778512	0.87[EUR][1000 genomes]
rs778513	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs778515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778516	0.86[EUR][1000 genomes]
rs778517	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778518	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778519	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs778520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778522	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778525	0.85[CEU][hapmap]
rs778527	0.85[CEU][hapmap]
rs801277	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs809640	0.87[EUR][1000 genomes]
rs875443	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9631541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9757330	0.81[CEU][hapmap]
rs9758590	0.81[CEU][hapmap]
rs9862734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23523200-23536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23524000-23534800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:23528000-23542200	Weak transcription	Right Ventricle	heart
6	chr3:23528600-23542200	Weak transcription	Primary B cells from cord blood	blood
7	chr3:23528600-23552200	Weak transcription	Ovary	ovary
8	chr3:23528800-23536600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:23528800-23536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:23530600-23542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:23531400-23536200	Weak transcription	Left Ventricle	heart
12	chr3:23531400-23536600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:23531400-23541600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:23532200-23534600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:23532200-23536600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:23532200-23536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:23532200-23547800	Weak transcription	NHLF	lung
18	chr3:23532400-23536600	Weak transcription	Osteobl	bone
19	chr3:23532400-23536800	Weak transcription	NHDF-Ad	bronchial
20	chr3:23532400-23537000	Weak transcription	HMEC	breast
21	chr3:23532600-23534200	Enhancers	Psoas Muscle	Psoas
22	chr3:23532600-23536600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:23532600-23536600	Weak transcription	NHEK	skin
24	chr3:23532600-23536800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:23532800-23536600	Weak transcription	A549	lung
26	chr3:23532800-23536800	Weak transcription	HUVEC	blood vessel
27	chr3:23533000-23535200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:23533400-23534800	Weak transcription	Aorta	Aorta
29	chr3:23533400-23537000	Enhancers	Fetal Heart	heart
30	chr3:23534000-23534800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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