Variant report

Variant	rs1488763
Chromosome Location	chr3:119884663-119884664
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119811496..119816423-chr3:119884642..119891818,9	MCF-7	breast:
2	chr3:119812784..119818369-chr3:119882594..119887208,9	MCF-7	breast:
3	chr3:119880098..119883232-chr3:119884308..119887648,3	K562	blood:
4	chr3:119872811..119874863-chr3:119883837..119886069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1074053	0.86[ASN][1000 genomes]
rs10934511	0.87[JPT][hapmap]
rs11707699	0.84[ASN][1000 genomes]
rs11712811	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13075809	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs13087908	0.93[CEU][hapmap]
rs13088757	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs13090279	0.86[ASN][1000 genomes]
rs13092071	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2035669	0.86[ASN][1000 genomes]
rs71327213	0.83[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1488763	GPR156	cis	Esophagus Muscularis	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119879400-119886000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:119879400-119886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:119880000-119888600	Weak transcription	A549	lung
5	chr3:119881600-119886200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:119881600-119888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:119881800-119886200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:119881800-119888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:119881800-119888600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:119882400-119888400	Weak transcription	Esophagus	oesophagus
11	chr3:119882400-119888400	Weak transcription	Hela-S3	cervix
12	chr3:119883000-119888400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:119883000-119888400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:119883000-119888400	Weak transcription	NHDF-Ad	bronchial
15	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
16	chr3:119883400-119886000	Weak transcription	HepG2	liver
17	chr3:119884200-119890400	Enhancers	Placenta	Placenta
18	chr3:119884400-119886200	Weak transcription	Fetal Brain Female	brain
19	chr3:119884600-119888600	Strong transcription	Fetal Stomach	stomach
20	chr3:119884600-119890400	Weak transcription	Adipose Nuclei	Adipose

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