Variant report

Variant	rs6542966
Chromosome Location	chr2:101140614-101140615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10166130	0.90[EUR][1000 genomes]
rs10166865	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs10175632	0.86[CHB][hapmap]
rs10180172	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10183360	0.81[EUR][1000 genomes]
rs10184491	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10185111	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10195487	0.81[EUR][1000 genomes]
rs10195943	0.83[CHB][hapmap]
rs10199745	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10199753	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10203739	0.87[EUR][1000 genomes]
rs10210508	0.85[CHB][hapmap]
rs10865040	0.81[EUR][1000 genomes]
rs11884644	0.88[EUR][1000 genomes]
rs11884976	0.81[CHB][hapmap]
rs11891670	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs11892956	0.89[EUR][1000 genomes]
rs11898188	0.81[CHB][hapmap]
rs11902961	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464855	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12465627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12466753	0.90[EUR][1000 genomes]
rs12475281	0.90[EUR][1000 genomes]
rs12475282	0.90[EUR][1000 genomes]
rs13385681	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs13388529	0.89[EUR][1000 genomes]
rs13389527	0.89[EUR][1000 genomes]
rs13393776	0.87[EUR][1000 genomes]
rs13408862	0.81[EUR][1000 genomes]
rs13411940	0.89[EUR][1000 genomes]
rs13414632	0.89[EUR][1000 genomes]
rs13414838	0.89[EUR][1000 genomes]
rs13415591	0.87[CHB][hapmap]
rs13420383	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs13421353	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13427972	0.88[EUR][1000 genomes]
rs13428749	0.87[EUR][1000 genomes]
rs13430695	0.89[EUR][1000 genomes]
rs1437968	0.87[CHB][hapmap]
rs1437974	0.87[CHB][hapmap]
rs17024335	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs17024409	0.87[EUR][1000 genomes]
rs17024441	0.90[EUR][1000 genomes]
rs17024477	0.81[ASN][1000 genomes]
rs2309858	0.87[EUR][1000 genomes]
rs2309859	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs2309860	0.87[EUR][1000 genomes]
rs2309861	0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs2309862	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes]
rs2309863	0.87[CHB][hapmap]
rs2309864	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs2871352	0.93[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes]
rs35031879	0.87[EUR][1000 genomes]
rs3748929	0.82[CHB][hapmap]
rs4581914	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs4630791	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs4632365	0.89[EUR][1000 genomes]
rs4633941	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs56304912	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57819301	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62155208	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542954	0.81[EUR][1000 genomes]
rs6542956	0.81[EUR][1000 genomes]
rs6542963	0.80[EUR][1000 genomes]
rs6542965	0.81[CHB][hapmap];0.89[MEX][hapmap]
rs6718127	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722896	0.81[CHB][hapmap]
rs6730933	0.82[CHB][hapmap]
rs6732569	0.82[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs6739721	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6745117	0.87[EUR][1000 genomes]
rs6747630	0.93[EUR][1000 genomes]
rs6755846	0.87[CHB][hapmap];0.89[MEX][hapmap]
rs6760452	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs750033	0.89[EUR][1000 genomes]
rs7578352	0.89[EUR][1000 genomes]
rs7592840	0.89[EUR][1000 genomes]
rs7593928	0.81[EUR][1000 genomes]
rs7594990	0.85[MEX][hapmap]
rs7596439	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs7596851	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs7597254	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598078	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7598339	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7599321	0.93[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs7602968	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605662	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs7606473	0.81[EUR][1000 genomes]
rs869840	0.86[EUR][1000 genomes]
rs9308837	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9653443	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542966	SEMA4C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101136800-101149000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:101140000-101141000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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