Variant report

Variant	rs8177262
Chromosome Location	chr3:133480652-133480653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:133470213-133490385	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:133480635-133480742	HepG2	liver:	n/a	n/a
3	FOSL2	chr3:133480329-133481334	HepG2	liver:	n/a	n/a
4	MYBL2	chr3:133480419-133481132	HepG2	liver:	n/a	n/a
5	CREB1	chr3:133480463-133481323	HepG2	liver:	n/a	n/a
6	MBD4	chr3:133480265-133482101	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133480532-133481275	HepG2	liver:	n/a	n/a
8	HEY1	chr3:133470261-133482084	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:133479434-133482047	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:133479493-133481361	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:133471516-133487597	HepG2	liver:	n/a	n/a
12	MBD4	chr3:133479369-133483413	HepG2	liver:	n/a	n/a
13	NFIC	chr3:133480477-133481222	HepG2	liver:	n/a	n/a
14	HEY1	chr3:133480476-133480891	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:133479294-133484913	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:133470633-133487808	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133380292..133382359-chr3:133479467..133482336,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPRB-3	chr3:133480371-133481207	NONHSAT092201

No data

Variant related genes	Relation type
TF	TF binding region
ENSG00000242337	Chromatin interaction
ENSG00000163781	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11710936	0.85[CHB][hapmap]
rs12490148	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs12595	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358024	0.82[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs1525889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1534165	0.85[CHB][hapmap]
rs1880669	0.86[CHD][hapmap]
rs2293375	0.85[CHB][hapmap]
rs2692695	0.86[CHD][hapmap]
rs34252038	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34805309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811647	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811658	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854760	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854761	1.00[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];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854762	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]
rs6439439	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762719	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794945	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs6797713	0.84[AMR][1000 genomes]
rs7638018	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8177224	0.81[CHD][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs8177240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177245	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177247	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177253	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177260	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177271	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177272	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177295	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9813689	0.80[EUR][1000 genomes]
rs9843728	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871148	0.80[EUR][1000 genomes]
rs9882812	0.80[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	nsv877508	chr3:133476852-133482662	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8177262	SRPRB	cis	multi-tissue	Pritchard
rs8177262	ANAPC13	cis	parietal	SCAN
rs8177262	SRPRB	cis	parietal	SCAN
rs8177262	SMN1	trans	lymphoblastoid	seeQTL
rs8177262	TOPBP1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133465600-133483000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:133473400-133480800	Strong transcription	Brain Inferior Temporal Lobe	brain
3	chr3:133475000-133487000	Weak transcription	Fetal Brain Male	brain
4	chr3:133475200-133480800	Strong transcription	HepG2	liver
5	chr3:133475200-133482800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:133477000-133490400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:133477800-133480800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:133478800-133482600	Weak transcription	Left Ventricle	heart
9	chr3:133479600-133482400	Strong transcription	Brain Cingulate Gyrus	brain
10	chr3:133480000-133482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:133480000-133483800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:133480200-133481000	Genic enhancers	Brain Hippocampus Middle	brain
13	chr3:133480400-133480800	Genic enhancers	Brain Anterior Caudate	brain
14	chr3:133480400-133486000	Genic enhancers	Brain Substantia Nigra	brain
15	chr3:133480600-133481200	Genic enhancers	Liver	Liver
16	chr3:133480600-133481200	Genic enhancers	Brain Angular Gyrus	brain

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