Variant report

Variant	rs2906893
Chromosome Location	chr12:1995699-1995700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10735005	0.84[GIH][hapmap]
rs10774003	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10848587	0.91[CHD][hapmap]
rs11062012	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[CHD][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1860051	0.88[EUR][1000 genomes]
rs2013064	0.84[GIH][hapmap]
rs2108633	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2108639	0.91[CHD][hapmap]
rs2190768	0.90[CEU][hapmap]
rs2190769	0.95[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs2190770	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs2370058	0.84[EUR][1000 genomes]
rs2429159	0.84[GIH][hapmap]
rs2906892	0.84[GIH][hapmap]
rs4765852	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4765864	0.95[CHD][hapmap]
rs7131989	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs758159	0.89[AFR][1000 genomes]
rs8181786	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2906893	FGF6	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1993000-1997000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:1993800-1996000	Enhancers	Stomach Mucosa	stomach
3	chr12:1994000-1996000	Enhancers	Gastric	stomach
4	chr12:1994200-1996000	Enhancers	K562	blood
5	chr12:1995400-1995800	Enhancers	HepG2	liver
6	chr12:1995600-1995800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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