Variant report

Variant	rs7653676
Chromosome Location	chr3:140061952-140061953
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140049779..140051880-chr3:140060017..140062705,2	K562	blood:
2	chr3:140059548..140062315-chr3:140087730..140089988,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1006877	0.85[GIH][hapmap]
rs1006878	0.82[GIH][hapmap]
rs1026775	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs1038157	0.82[CEU][hapmap]
rs1154766	0.85[GIH][hapmap]
rs11706485	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708993	0.81[GIH][hapmap]
rs11716346	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13099847	0.94[CHB][hapmap]
rs1479874	0.83[EUR][1000 genomes]
rs1479877	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1479879	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1531637	0.81[CEU][hapmap]
rs1564395	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1564397	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17345403	0.88[ASW][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes]
rs1964547	0.92[EUR][1000 genomes]
rs35501742	0.84[EUR][1000 genomes]
rs3925729	0.82[EUR][1000 genomes]
rs3943277	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4410413	0.94[CHB][hapmap]
rs4642081	0.94[CHB][hapmap]
rs4683488	0.94[CHB][hapmap]
rs4683821	0.82[EUR][1000 genomes]
rs6762256	0.81[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6766533	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6766541	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs6786128	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs6786368	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6797448	0.82[CEU][hapmap]
rs6797652	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs6810326	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs7610675	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7611205	0.83[GIH][hapmap]
rs7618673	0.94[CHB][hapmap]
rs7624142	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7630996	0.81[GIH][hapmap]
rs899622	0.87[CHB][hapmap]
rs9289603	0.81[CEU][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs9817769	0.94[CHB][hapmap]
rs9832534	0.83[GIH][hapmap]
rs9871764	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[MKK][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873058	0.82[CEU][hapmap]
rs987486	0.81[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs999819	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv460867	chr3:140007294-140180563	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv591861	chr3:140007294-140180563	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv818169	chr3:140014763-140182046	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1001430	chr3:140016999-140186498	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv998953	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv536731	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv829741	chr3:140021063-140183294	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140043000-140068600	Weak transcription	HSMMtube	muscle
2	chr3:140058800-140062000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:140059400-140062200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:140059600-140062000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:140059800-140062000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:140060000-140062000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:140060000-140062000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:140060600-140062800	Weak transcription	Ovary	ovary
9	chr3:140061400-140062000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:140061600-140062000	Enhancers	HMEC	breast
11	chr3:140061800-140062800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:140061800-140063600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:140061800-140064000	Enhancers	NHEK	skin
14	chr3:140061800-140065200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:140061800-140066000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:140061800-140084800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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