Variant report

Variant	rs3804320
Chromosome Location	chr6:24177923-24177924
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11751907	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11969397	0.87[ASN][1000 genomes]
rs16888748	0.91[ASN][1000 genomes]
rs1936389	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747781	0.80[GIH][hapmap]
rs3789219	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449614	0.82[CEU][hapmap]
rs4607425	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs60661883	0.86[ASN][1000 genomes]
rs62400343	0.92[ASN][1000 genomes]
rs6456593	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456594	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6937665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6938529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356929	0.92[ASN][1000 genomes]
rs9358752	0.87[ASN][1000 genomes]
rs9358753	1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9379646	0.87[ASN][1000 genomes]
rs9393532	0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9393533	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9393534	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3804320	HIST1H3G	cis	cerebellum	SCAN
rs3804320	HIST1H2AK	cis	parietal	SCAN
rs3804320	HIST1H3C	cis	cerebellum	SCAN
rs3804320	HIST1H1D	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr6:24164400-24183800	Weak transcription	Pancreas	Pancrea
3	chr6:24171600-24182800	Weak transcription	Fetal Intestine Small	intestine
4	chr6:24172800-24194800	Weak transcription	Fetal Intestine Large	intestine
5	chr6:24174000-24179600	Strong transcription	HepG2	liver
6	chr6:24177600-24179600	Strong transcription	Fetal Kidney	kidney
7	chr6:24177800-24198400	Weak transcription	A549	lung

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