Variant report

Variant	rs6886626
Chromosome Location	chr5:42897848-42897849
allele	A/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	chr5:42897629-42897887	IMR90	lung:	n/a	chr5:42897787-42897798
2	CEBPB	chr5:42897629-42897949	HepG2	liver:	n/a	chr5:42897787-42897798
3	CEBPB	chr5:42897684-42897942	K562	blood:	n/a	chr5:42897787-42897798

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42897117..42899621-chr5:43119844..43121464,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEPP1-3	chr5:42897364-42897934	NONHSAT101232

Variant related genes	Relation type
ENSG00000249092	TF binding region
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10036147	0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10036468	0.91[ASN][1000 genomes]
rs10044301	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10053947	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10061198	0.91[ASN][1000 genomes]
rs10068961	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10072017	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12655096	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[ASN][1000 genomes]
rs12658770	0.87[ASN][1000 genomes]
rs12659760	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13156119	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13354920	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs160330	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188793	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902100	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2098715	0.95[ASN][1000 genomes]
rs2548362	0.83[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2548364	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548365	0.90[EUR][1000 genomes]
rs2548366	0.92[EUR][1000 genomes]
rs2603622	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2603624	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28415991	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs309932	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309934	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309935	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309942	0.89[EUR][1000 genomes]
rs315246	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs315253	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs315263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34917335	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34981544	0.91[ASN][1000 genomes]
rs371261	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs378235	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs378344	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388214	0.94[ASN][1000 genomes]
rs420550	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435312	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs446294	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4482913	0.91[ASN][1000 genomes]
rs4513706	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs453436	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451649	0.91[ASN][1000 genomes]
rs6451650	0.91[ASN][1000 genomes]
rs6451651	0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6451652	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6451653	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451654	0.84[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6864892	0.98[ASN][1000 genomes]
rs6867854	0.89[ASN][1000 genomes]
rs6875237	0.91[ASN][1000 genomes]
rs6881608	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6885355	0.91[ASN][1000 genomes]
rs6895458	0.91[ASN][1000 genomes]
rs6895751	0.91[ASN][1000 genomes]
rs71627562	0.97[ASN][1000 genomes]
rs71627563	0.97[ASN][1000 genomes]
rs7701142	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7721545	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9885101	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
7	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
8	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv980936	chr5:42894375-42930741	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42894400-42902000	Weak transcription	Right Atrium	heart
2	chr5:42894600-42908600	Weak transcription	Pancreas	Pancrea
3	chr5:42897600-42898200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links