Variant report

Variant	rs3966561
Chromosome Location	chr7:39923125-39923126
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	chr7:39922523..39924083-chr7:40170762..40172465,2	K562	blood:
2	chr7:39920454..39923588-chr7:39927259..39930788,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242855	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10225311	0.92[ASN][1000 genomes]
rs10270355	0.86[ASN][1000 genomes]
rs11760665	0.83[AFR][1000 genomes]
rs11973720	0.84[ASN][1000 genomes]
rs11975808	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11983868	0.86[ASN][1000 genomes]
rs12701774	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12701777	0.81[AFR][1000 genomes]
rs12701778	0.92[ASN][1000 genomes]
rs1523711	0.92[ASN][1000 genomes]
rs1608500	0.86[ASN][1000 genomes]
rs2049350	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2091092	0.90[ASN][1000 genomes]
rs2329608	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2329609	0.92[ASN][1000 genomes]
rs2329610	0.92[ASN][1000 genomes]
rs4720343	0.92[ASN][1000 genomes]
rs4723914	0.92[ASN][1000 genomes]
rs4723915	0.92[ASN][1000 genomes]
rs6462952	0.92[ASN][1000 genomes]
rs6462953	0.91[ASN][1000 genomes]
rs6947780	0.92[ASN][1000 genomes]
rs6949575	0.92[ASN][1000 genomes]
rs6957432	0.92[ASN][1000 genomes]
rs6969026	0.92[ASN][1000 genomes]
rs6979770	0.92[ASN][1000 genomes]
rs72589780	0.92[ASN][1000 genomes]
rs72589783	0.86[ASN][1000 genomes]
rs7787480	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7789497	0.92[ASN][1000 genomes]
rs9638946	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv887974	chr7:39827400-39956829	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv966783	chr7:39913292-39923658	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39922800-39924000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:39922800-39927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links