Variant report

Variant	rs62260717
Chromosome Location	chr3:49833029-49833030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49828367..49831319-chr3:49832750..49837135,3	MCF-7	breast:
2	chr3:49824316..49827108-chr3:49830992..49833556,2	MCF-7	breast:
3	chr3:49832936..49834701-chr3:49956743..49959111,2	MCF-7	breast:
4	chr3:49832962..49835911-chr3:49836765..49838796,2	K562	blood:

Variant related genes	Relation type
ENSG00000187492	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11130223	0.88[EUR][1000 genomes]
rs11130230	0.80[EUR][1000 genomes]
rs11130237	0.80[EUR][1000 genomes]
rs11130239	0.80[EUR][1000 genomes]
rs11130240	0.82[EUR][1000 genomes]
rs11916261	0.80[EUR][1000 genomes]
rs11923132	0.80[EUR][1000 genomes]
rs11925156	0.80[EUR][1000 genomes]
rs12486808	0.84[EUR][1000 genomes]
rs12486832	0.84[EUR][1000 genomes]
rs12489386	0.88[EUR][1000 genomes]
rs12490944	0.84[EUR][1000 genomes]
rs12493565	0.84[EUR][1000 genomes]
rs12495831	0.88[EUR][1000 genomes]
rs12629129	0.84[EUR][1000 genomes]
rs12629677	0.84[EUR][1000 genomes]
rs12630917	0.80[EUR][1000 genomes]
rs12630959	0.80[EUR][1000 genomes]
rs12631306	0.80[EUR][1000 genomes]
rs12631309	0.80[EUR][1000 genomes]
rs12631608	0.80[EUR][1000 genomes]
rs12636669	0.80[EUR][1000 genomes]
rs12637222	0.80[EUR][1000 genomes]
rs12637457	0.84[EUR][1000 genomes]
rs12637681	0.85[EUR][1000 genomes]
rs12638046	0.84[EUR][1000 genomes]
rs1317215	0.88[EUR][1000 genomes]
rs13326300	0.88[EUR][1000 genomes]
rs28478136	0.88[EUR][1000 genomes]
rs41290716	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs41291716	0.84[EUR][1000 genomes]
rs55643042	0.88[EUR][1000 genomes]
rs57009357	0.84[EUR][1000 genomes]
rs57575459	0.84[EUR][1000 genomes]
rs58025924	0.84[EUR][1000 genomes]
rs58621288	0.80[EUR][1000 genomes]
rs58766761	0.84[EUR][1000 genomes]
rs61491513	0.80[EUR][1000 genomes]
rs61729114	0.84[EUR][1000 genomes]
rs62260756	0.88[EUR][1000 genomes]
rs62261251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62262060	0.88[EUR][1000 genomes]
rs62262095	0.84[EUR][1000 genomes]
rs62262096	0.84[EUR][1000 genomes]
rs62262099	0.84[EUR][1000 genomes]
rs62262100	0.84[EUR][1000 genomes]
rs62262105	0.80[EUR][1000 genomes]
rs62262116	0.80[EUR][1000 genomes]
rs62262117	0.80[EUR][1000 genomes]
rs62262138	0.80[EUR][1000 genomes]
rs62262144	0.80[EUR][1000 genomes]
rs62262145	0.80[EUR][1000 genomes]
rs62262148	0.84[EUR][1000 genomes]
rs62262670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62262676	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262682	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262683	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262727	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62263578	0.84[EUR][1000 genomes]
rs6797500	0.88[EUR][1000 genomes]
rs9813644	0.88[EUR][1000 genomes]
rs9859813	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus
2	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
3	chr3:49832400-49833200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49832400-49833400	Flanking Active TSS	HepG2	liver
5	chr3:49832600-49833400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49832600-49833400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:49832800-49833600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:49832800-49833600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr3:49832800-49834400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:49833000-49833400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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