Variant report

Variant	rs17641650
Chromosome Location	chr19:40078431-40078432
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	CEBPB	chr19:40078167-40078558	MCF-7	breast:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
2	CEBPB	chr19:40078296-40078611	A549	lung:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
3	CEBPB	chr19:40078223-40078548	MCF-7	breast:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
4	STAT3	chr19:40078325-40078525	MCF10A-Er-Src	breast:	n/a	chr19:40078431-40078438 chr19:40078457-40078465
5	FOS	chr19:40078137-40078502	MCF10A-Er-Src	breast:	n/a	chr19:40078319-40078329 chr19:40078320-40078327 chr19:40078319-40078329 chr19:40078320-40078329 chr19:40078318-40078330 chr19:40078319-40078328
6	CEBPB	chr19:40078272-40078550	Hela-S3	cervix:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
7	CEBPB	chr19:40078292-40078584	HepG2	liver:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
8	FOS	chr19:40078122-40078548	MCF10A-Er-Src	breast:	n/a	chr19:40078319-40078329 chr19:40078320-40078327 chr19:40078319-40078329 chr19:40078320-40078329 chr19:40078318-40078330 chr19:40078319-40078328
9	CEBPB	chr19:40078295-40078593	IMR90	lung:	n/a	chr19:40078454-40078465 chr19:40078456-40078465 chr19:40078455-40078466
10	FOS	chr19:40078182-40078500	MCF10A-Er-Src	breast:	n/a	chr19:40078319-40078329 chr19:40078320-40078327 chr19:40078319-40078329 chr19:40078320-40078329 chr19:40078318-40078330 chr19:40078319-40078328
11	REST	chr19:40077888-40082568	PANC-1	pancreas:	n/a	chr19:40081090-40081098 chr19:40081098-40081112 chr19:40081097-40081106 chr19:40081092-40081112 chr19:40081092-40081101 chr19:40081092-40081112 chr19:40081093-40081111 chr19:40081092-40081105 chr19:40081092-40081112
12	MYC	chr19:40078249-40078484	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr19:40078226-40078452	MCF10A-Er-Src	breast:	n/a	chr19:40078431-40078438 chr19:40078319-40078328
14	FOS	chr19:40078192-40078498	MCF10A-Er-Src	breast:	n/a	chr19:40078319-40078329 chr19:40078320-40078327 chr19:40078319-40078329 chr19:40078320-40078329 chr19:40078318-40078330 chr19:40078319-40078328
15	REST	chr19:40077888-40082618	PANC-1	pancreas:	n/a	chr19:40081090-40081098 chr19:40081098-40081112 chr19:40081097-40081106 chr19:40081092-40081112 chr19:40081092-40081101 chr19:40081092-40081112 chr19:40081093-40081111 chr19:40081092-40081105 chr19:40081092-40081112

Variant related genes	Relation type
RPS29P25	TF binding region
RPS29P24	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12608773	0.81[EUR][1000 genomes]
rs12609985	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610751	0.90[CEU][hapmap]
rs12611125	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs12972285	0.81[EUR][1000 genomes]
rs12972675	0.81[EUR][1000 genomes]
rs12980249	0.80[EUR][1000 genomes]
rs17795475	0.90[CEU][hapmap];0.87[GIH][hapmap]
rs1836011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126123	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34355544	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34856311	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs34885802	0.81[EUR][1000 genomes]
rs35038530	0.81[EUR][1000 genomes]
rs4608447	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803258	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs67832846	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247184	0.82[EUR][1000 genomes]
rs7247218	0.82[EUR][1000 genomes]
rs7257553	0.81[EUR][1000 genomes]
rs7257904	0.81[EUR][1000 genomes]
rs7258348	0.82[EUR][1000 genomes]
rs7507648	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv34120	chr19:40044635-40131820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17641650	EID2B	cis	lymphoblastoid	seeQTL
rs17641650	GSK3A	cis	cerebellum	SCAN
rs17641650	MRPS12	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40078000-40079400	Enhancers	HMEC	breast
2	chr19:40078200-40079200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:40078200-40079200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:40078200-40079200	Weak transcription	Placenta	Placenta

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