Variant report

Variant	rs9658810
Chromosome Location	chr1:197472070-197472071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494756	0.90[ASN][1000 genomes]
rs10801607	0.82[EUR][1000 genomes]
rs10801609	0.85[ASN][1000 genomes]
rs10922231	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs10922236	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10922244	0.81[ASN][1000 genomes]
rs10922260	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1135810	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs12042609	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1337166	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1345529	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1923759	0.81[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs2111930	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2287537	0.91[ASN][1000 genomes]
rs2494268	0.81[YRI][hapmap]
rs2821102	0.84[YRI][hapmap]
rs4026508	0.80[EUR][1000 genomes]
rs4026513	0.87[EUR][1000 genomes]
rs4026514	0.82[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.81[ASN][1000 genomes]
rs4147323	0.85[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4274099	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4418639	0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4604725	0.85[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs6691216	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs7534863	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs927510	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs9787082	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][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	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv4010	chr1:197471463-197511397	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9658810	LHX2	trans	parietal	SCAN
rs9658810	DENND1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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