Variant report

Variant	rs6962939
Chromosome Location	chr7:7524226-7524227
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7521538..7523619-chr7:7523634..7525398,2	MCF-7	breast:
2	chr7:7521873..7525191-chr7:7530979..7533379,3	MCF-7	breast:
3	chr7:7523488..7525479-chr7:7527617..7529829,2	K562	blood:
4	chr7:7517874..7521544-chr7:7521578..7525558,4	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10085718	1.00[ASN][1000 genomes]
rs1013002	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs1016028	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10251718	1.00[JPT][hapmap]
rs11773679	0.82[CEU][hapmap]
rs11976831	0.81[EUR][1000 genomes]
rs11983756	0.82[CEU][hapmap]
rs12535954	1.00[ASN][1000 genomes]
rs12702633	1.00[JPT][hapmap]
rs1294600	0.81[EUR][1000 genomes]
rs13225575	1.00[JPT][hapmap]
rs13227682	1.00[JPT][hapmap]
rs17167617	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17169196	1.00[JPT][hapmap]
rs17524233	1.00[JPT][hapmap]
rs2108064	0.82[CEU][hapmap]
rs2108067	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2190248	0.81[EUR][1000 genomes]
rs2348045	1.00[JPT][hapmap]
rs2348047	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2881888	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs28847278	1.00[ASN][1000 genomes]
rs28916005	1.00[JPT][hapmap]
rs3757532	0.82[CEU][hapmap]
rs4035104	0.95[EUR][1000 genomes]
rs4380838	0.82[CEU][hapmap]
rs4720741	0.82[CEU][hapmap]
rs4725005	0.82[CEU][hapmap]
rs6463696	1.00[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs6463702	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6946022	0.82[CEU][hapmap]
rs6946425	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs6948157	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6957976	0.82[CEU][hapmap]
rs6958110	1.00[CEU][hapmap]
rs6964397	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6964593	1.00[JPT][hapmap]
rs6974820	1.00[JPT][hapmap]
rs6980052	1.00[JPT][hapmap]
rs73346346	1.00[ASN][1000 genomes]
rs73347196	1.00[ASN][1000 genomes]
rs73347201	1.00[ASN][1000 genomes]
rs73348905	1.00[ASN][1000 genomes]
rs7783239	0.82[CEU][hapmap]
rs7787580	1.00[JPT][hapmap]
rs7789187	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7789287	0.82[CEU][hapmap]
rs7793870	1.00[JPT][hapmap]
rs7796709	0.81[EUR][1000 genomes]
rs7801367	1.00[ASN][1000 genomes]
rs7806046	0.82[CEU][hapmap]
rs7808788	0.81[EUR][1000 genomes]
rs9640043	0.81[EUR][1000 genomes]
rs9640045	0.82[CEU][hapmap]
rs972600	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv606043	chr7:7473563-7571420	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6962939	FAM184A	trans	lymphoblastoid	seeQTL
rs6962939	VNN1	trans	lymphoblastoid	seeQTL
rs6962939	SUCNR1	trans	lymphoblastoid	seeQTL
rs6962939	C20orf30	trans	lymphoblastoid	seeQTL
rs6962939	TNN	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7514400-7527400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:7519200-7529600	Weak transcription	Fetal Kidney	kidney
3	chr7:7521800-7529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links