Variant report

Variant	rs1856908
Chromosome Location	chr10:96732731-96732732
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1200313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12772675	0.84[ASN][1000 genomes]
rs12772884	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs1322181	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1555474	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1934953	0.84[MEX][hapmap]
rs1934960	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1934964	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1934965	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1934969	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1998321	0.80[ASN][1000 genomes]
rs2096069	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104161	0.81[JPT][hapmap]
rs2253635	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2475376	0.81[LWK][hapmap];0.89[YRI][hapmap]
rs2860906	0.89[ASN][1000 genomes]
rs35687798	0.84[ASN][1000 genomes]
rs3740504	0.83[ASN][1000 genomes]
rs4362080	0.82[JPT][hapmap]
rs4617515	0.91[JPT][hapmap]
rs4917623	0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs4917641	0.84[ASN][1000 genomes]
rs4918758	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4918766	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6583963	0.81[ASN][1000 genomes]
rs6583968	0.84[MEX][hapmap]
rs7073165	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7078102	0.80[AMR][1000 genomes]
rs7079343	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7083767	0.89[ASN][1000 genomes]
rs7095531	0.84[MEX][hapmap]
rs7475054	0.87[ASN][1000 genomes]
rs7895223	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7899661	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7903917	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915414	0.91[JPT][hapmap]
rs7916649	0.83[CHD][hapmap];0.91[JPT][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv551962	chr10:96680265-96734339	Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv551963	chr10:96720262-96743943	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1856908	PPP1R3C	cis	parietal	SCAN
rs1856908	FXYD6	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96718600-96737600	Weak transcription	Fetal Intestine Large	intestine
2	chr10:96730600-96738600	Strong transcription	Liver	Liver

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