Variant report

Variant	rs16888748
Chromosome Location	chr6:24170975-24170976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11751907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11969397	0.94[ASN][1000 genomes]
rs13208582	0.81[ASN][1000 genomes]
rs1936389	0.91[ASN][1000 genomes]
rs3789219	0.92[ASN][1000 genomes]
rs3804320	0.91[ASN][1000 genomes]
rs4449614	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4607425	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs60661883	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62400343	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456593	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6456594	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6937665	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6938529	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9356929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358752	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358753	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379646	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393532	0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv1798372	chr6:24158542-24181477	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv601146	chr6:24166233-24215665	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv3374244	chr6:24170968-24171803	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16888748	HIST1H2BG	cis	parietal	SCAN
rs16888748	HIST1H3J	cis	cerebellum	SCAN
rs16888748	HIST1H4C	cis	parietal	SCAN
rs16888748	HIST1H1D	cis	parietal	SCAN
rs16888748	HIST1H2AK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24153800-24200800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:24163600-24177600	Weak transcription	Fetal Kidney	kidney
3	chr6:24164400-24183800	Weak transcription	Pancreas	Pancrea
4	chr6:24170000-24171600	Weak transcription	HepG2	liver

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