Variant report

Variant	rs787201
Chromosome Location	chr3:120021481-120021482
allele	G/T
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	JUND	chr3:120021243-120021546	K562	blood:	n/a	chr3:120021430-120021440 chr3:120021427-120021438 chr3:120021431-120021439 chr3:120021431-120021439 chr3:120021432-120021439 chr3:120021430-120021440 chr3:120021430-120021440
2	FOS	chr3:120021300-120021570	MCF10A-Er-Src	breast:	n/a	chr3:120021430-120021440 chr3:120021427-120021438 chr3:120021431-120021439 chr3:120021431-120021439 chr3:120021432-120021439 chr3:120021430-120021440 chr3:120021430-120021440

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120018316..120022593-chr3:120022628..120028274,5	MCF-7	breast:
2	chr3:120020374..120022764-chr3:120067008..120069346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240882	TF binding region
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000240882	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1085612	0.89[ASN][1000 genomes]
rs1085613	0.89[ASN][1000 genomes]
rs1085625	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1092743	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs1092829	0.89[ASN][1000 genomes]
rs1147682	0.81[ASN][1000 genomes]
rs1147687	0.80[CHB][hapmap]
rs1147692	0.87[CHB][hapmap]
rs1259290	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1356112	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs1515574	0.94[JPT][hapmap]
rs1515576	0.84[ASN][1000 genomes]
rs1621291	0.80[CHB][hapmap]
rs1716838	0.86[CEU][hapmap]
rs1716839	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs1716840	0.80[CHB][hapmap]
rs1733324	0.91[CEU][hapmap]
rs1733329	0.86[CHB][hapmap]
rs2138259	0.85[ASN][1000 genomes]
rs2638592	0.89[ASN][1000 genomes]
rs2702156	0.87[CHB][hapmap]
rs2943754	0.86[CHB][hapmap]
rs3914498	0.81[JPT][hapmap]
rs6438576	0.86[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6438578	0.86[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6438579	0.85[ASN][1000 genomes]
rs7622363	0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs787197	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs787199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787202	0.86[CHB][hapmap]
rs787210	0.89[ASN][1000 genomes]
rs805080	0.95[ASN][1000 genomes]
rs810888	0.96[ASN][1000 genomes]
rs813698	0.93[ASN][1000 genomes]
rs939499	0.85[ASN][1000 genomes]
rs9851825	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs787201	GPR156	cis	Esophagus Muscularis	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120019800-120022800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:120020800-120021600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120020800-120021600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:120020800-120022600	Enhancers	Adipose Nuclei	Adipose
5	chr3:120021000-120022000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:120021000-120022000	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:120021000-120022200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:120021000-120023600	Weak transcription	Fetal Kidney	kidney
9	chr3:120021200-120021800	Enhancers	NHDF-Ad	bronchial
10	chr3:120021200-120023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:120021200-120025600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:120021400-120023200	Weak transcription	Placenta	Placenta
13	chr3:120021400-120024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:120021400-120025800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:120021400-120026000	Weak transcription	Aorta	Aorta

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