Variant report

Variant	rs210196
Chromosome Location	chr6:33507723-33507724
allele	C/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	FOS	chr6:33507623-33508229	MCF10A-Er-Src	breast:	n/a	chr6:33507710-33507721
2	STAT3	chr6:33507651-33508222	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
3	STAT3	chr6:33507660-33508131	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
4	CEBPB	chr6:33507674-33507854	K562	blood:	n/a	n/a
5	STAT3	chr6:33507643-33508255	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
6	STAT3	chr6:33507623-33508222	MCF10A-Er-Src	breast:	n/a	chr6:33507774-33507785
7	FOS	chr6:33507661-33508236	MCF10A-Er-Src	breast:	n/a	chr6:33507710-33507721

Variant related genes	Relation type
RN7SL26P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs17627049	1.00[CHB][hapmap]
rs1794687	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs191902	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs210177	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs210178	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs210180	0.90[EUR][1000 genomes]
rs210182	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210183	0.89[EUR][1000 genomes]
rs210184	0.89[EUR][1000 genomes]
rs210185	0.89[EUR][1000 genomes]
rs210186	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210187	0.87[EUR][1000 genomes]
rs210192	0.86[EUR][1000 genomes]
rs210197	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]
rs210202	0.84[CEU][hapmap]
rs210203	0.88[CEU][hapmap];0.95[GIH][hapmap]
rs210207	0.88[CEU][hapmap]
rs210209	0.88[CEU][hapmap]
rs367408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs367897	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs368429	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs371155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs372469	0.88[EUR][1000 genomes]
rs372846	0.88[EUR][1000 genomes]
rs380163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs383936	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs386879	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3916269	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs396516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404778	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs405126	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435945	0.95[LWK][hapmap];1.00[YRI][hapmap]
rs447418	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs449242	0.96[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73404347	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461874	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9469481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9469483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs210196	FTSJD2	cis	cerebellum	SCAN
rs210196	CDKN1A	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr6:33507400-33507800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr6:33507600-33508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:33507600-33508000	Enhancers	HMEC	breast
5	chr6:33507600-33508200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:33507600-33508200	Enhancers	NHEK	skin
7	chr6:33507600-33508600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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