Variant report

Variant	rs346509
Chromosome Location	chr4:86835805-86835806
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	POLR2A	chr4:86835747-86836152	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000265774	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1027942	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11097082	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13121761	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17011166	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs186969	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904084	0.95[EUR][1000 genomes]
rs346510	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs346513	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs346516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs346517	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs346520	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs346521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806762	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs4326006	0.84[YRI][hapmap]
rs4348086	0.94[YRI][hapmap]
rs6531876	0.89[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7663884	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7664621	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7685851	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs958887	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9790515	0.81[AMR][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	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879519	chr4:86786204-86871282	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv2753470	chr4:86804078-86844350	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86791200-86844400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:86808200-86846000	Weak transcription	HUVEC	blood vessel
3	chr4:86815800-86842800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:86826800-86845400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:86827600-86850600	Weak transcription	Spleen	Spleen
6	chr4:86829600-86843800	Weak transcription	Primary B cells from cord blood	blood
7	chr4:86831200-86851000	Weak transcription	Aorta	Aorta
8	chr4:86832400-86842800	Weak transcription	Pancreas	Pancrea
9	chr4:86832400-86843800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:86834000-86836200	Enhancers	Fetal Intestine Large	intestine
11	chr4:86834200-86836000	Enhancers	Fetal Intestine Small	intestine
12	chr4:86834200-86836400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr4:86834400-86836000	Enhancers	Fetal Kidney	kidney
14	chr4:86834600-86836200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr4:86834600-86841000	Weak transcription	A549	lung
16	chr4:86834800-86836000	Enhancers	Duodenum Mucosa	Duodenum
17	chr4:86835600-86840400	Weak transcription	Stomach Mucosa	stomach

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