Variant report

Variant	rs4854762
Chromosome Location	chr3:133499063-133499064
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	POLR2A	chr3:133493379-133499245	HepG2	liver:	n/a	n/a
2	REST	chr3:133498880-133499095	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr3:133498287-133499194	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:133498921-133499179	HepG2	liver:	n/a	n/a
5	MBD4	chr3:133497618-133500050	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:133493570-133500066	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133492554-133499992	HepG2	liver:	n/a	n/a
8	NFIC	chr3:133498565-133499296	HepG2	liver:	n/a	n/a
9	MYBL2	chr3:133498065-133499680	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:133485083-133500247	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:133490522-133500229	HepG2	liver:	n/a	n/a
12	MBD4	chr3:133498030-133499159	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:133497985-133499246	HepG2	liver:	n/a	n/a
14	HEY1	chr3:133497120-133499351	HepG2	liver:	n/a	n/a
15	FOSL2	chr3:133498092-133499262	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SRPRB	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12490148	0.81[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12595	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079426	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1358024	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs1525889	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1830083	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1830084	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1880669	0.86[CHD][hapmap]
rs2692695	0.87[CHD][hapmap]
rs34252038	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34805309	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35332919	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3811647	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811658	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854760	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854761	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439439	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6762719	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794945	0.80[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7638018	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177224	0.86[MEX][hapmap]
rs8177240	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177245	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177247	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177248	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177252	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177253	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177256	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177259	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177260	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177261	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177262	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177271	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8177272	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8177295	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8177297	0.83[ASN][1000 genomes]
rs9813689	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9843728	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871148	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9882812	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4018	chr3:133485867-133530668	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4854762	TOPBP1	cis	parietal	SCAN
rs4854762	SRPRB	cis	multi-tissue	Pritchard
rs4854762	SRPRB	cis	parietal	SCAN
rs4854762	ANAPC13	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133486000-133499200	Strong transcription	Brain Substantia Nigra	brain
2	chr3:133496200-133500200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:133497400-133502600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:133498000-133499600	Weak transcription	HepG2	liver
5	chr3:133498200-133500400	Weak transcription	Liver	Liver
6	chr3:133498400-133503400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:133498600-133499200	Enhancers	K562	blood
8	chr3:133498600-133505800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:133498600-133510400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:133498800-133508000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:133499000-133505200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:133499000-133510800	Weak transcription	Brain Hippocampus Middle	brain

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