Variant report

Variant	rs56160793
Chromosome Location	chr6:161339651-161339652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr6:161339622-161339783	HepG2	liver:	n/a	chr6:161339720-161339736
2	CEBPB	chr6:161339489-161339750	Hela-S3	cervix:	n/a	n/a
3	NR2F2	chr6:161339347-161339730	MCF-7	breast:	n/a	chr6:161339415-161339430
4	FOS	chr6:161339427-161339652	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr6:161339357-161339673	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr6:161339555-161339669	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr6:161339453-161339666	MCF-7	breast:	n/a	n/a
8	GATA1	chr6:161339577-161340108	K562	blood:	n/a	chr6:161339959-161339975

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPA-3	chr6:161339469-161339681	ENSG00000224371

Variant related genes	Relation type
ENSG00000224371	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11751714	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753115	1.00[ASN][1000 genomes]
rs11754459	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758620	1.00[ASN][1000 genomes]
rs11759366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963931	1.00[ASN][1000 genomes]
rs2096408	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2275926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56820519	1.00[ASN][1000 genomes]
rs60465142	1.00[ASN][1000 genomes]
rs6914092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017797	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73019757	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019758	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019760	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019762	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019772	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73021743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750449	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr6:161334200-161347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161338000-161341800	Enhancers	Fetal Intestine Small	intestine
3	chr6:161338600-161340200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:161338600-161340600	Enhancers	Placenta	Placenta
5	chr6:161338600-161341600	Enhancers	Fetal Intestine Large	intestine
6	chr6:161338800-161341600	Enhancers	Stomach Mucosa	stomach
7	chr6:161339000-161340400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:161339400-161339800	Flanking Active TSS	Liver	Liver
9	chr6:161339400-161340000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:161339400-161340000	Flanking Active TSS	HepG2	liver
11	chr6:161339400-161340800	Enhancers	Pancreas	Pancrea
12	chr6:161339400-161341200	Enhancers	Duodenum Mucosa	Duodenum
13	chr6:161339400-161341600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:161339400-161341600	Enhancers	Hela-S3	cervix
15	chr6:161339400-161341600	Enhancers	HMEC	breast
16	chr6:161339600-161340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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