Variant report

Variant	rs210197
Chromosome Location	chr6:33507991-33507992
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	FOSL2	chr6:33507860-33508228	HepG2	liver:	n/a	n/a
2	FOS	chr6:33507623-33508229	MCF10A-Er-Src	breast:	n/a	chr6:33507710-33507721
3	STAT3	chr6:33507651-33508222	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
4	STAT3	chr6:33507660-33508131	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
5	BATF	chr6:33507961-33508146	GM12878	blood:	n/a	chr6:33508060-33508071
6	FOSL2	chr6:33507880-33508240	MCF-7	breast:	n/a	n/a
7	STAT3	chr6:33507643-33508255	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
8	JUND	chr6:33507924-33508177	HepG2	liver:	n/a	chr6:33508058-33508069
9	STAT3	chr6:33507623-33508222	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
10	FOS	chr6:33507879-33508230	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:33507661-33508236	MCF10A-Er-Src	breast:	n/a	chr6:33507710-33507721
12	FOS	chr6:33507761-33508229	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RN7SL26P	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs17627049	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1794687	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191901	0.83[AMR][1000 genomes]
rs191902	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210151	0.83[AMR][1000 genomes]
rs210177	0.91[EUR][1000 genomes]
rs210178	0.92[EUR][1000 genomes]
rs210180	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs210182	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210183	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs210184	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs210185	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs210186	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210187	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs210192	0.91[EUR][1000 genomes]
rs210196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210201	0.80[EUR][1000 genomes]
rs210202	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs210203	0.88[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs210204	0.80[EUR][1000 genomes]
rs210205	0.82[AMR][1000 genomes]
rs210206	0.80[EUR][1000 genomes]
rs210207	0.88[CEU][hapmap]
rs210208	0.83[AMR][1000 genomes]
rs210209	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs210210	0.83[AMR][1000 genomes]
rs367408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368429	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs368716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371155	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372469	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs372846	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs380163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383936	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386879	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916269	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs396516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404778	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405126	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447418	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449242	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73404347	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461874	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv2763548	chr6:33496201-33524779	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs210197	BAK1	cis	lymphoblastoid	seeQTL
rs210197	LHFPL5	cis	parietal	SCAN
rs210197	CDKN1A	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33501600-33512800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:33507600-33508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:33507600-33508000	Enhancers	HMEC	breast
4	chr6:33507600-33508200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:33507600-33508200	Enhancers	NHEK	skin
6	chr6:33507600-33508600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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