Variant report

Variant	rs10951647
Chromosome Location	chr7:41237214-41237215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10214988	0.82[EUR][1000 genomes]
rs10214990	0.82[EUR][1000 genomes]
rs10215332	0.82[EUR][1000 genomes]
rs10215556	0.80[EUR][1000 genomes]
rs10215561	0.80[EUR][1000 genomes]
rs10215670	0.82[EUR][1000 genomes]
rs10225564	0.82[EUR][1000 genomes]
rs10225707	0.82[EUR][1000 genomes]
rs10230756	0.82[EUR][1000 genomes]
rs10233411	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10238779	0.80[EUR][1000 genomes]
rs10242681	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10281338	0.82[EUR][1000 genomes]
rs10951648	0.83[EUR][1000 genomes]
rs11505532	0.80[EUR][1000 genomes]
rs11760865	0.82[EUR][1000 genomes]
rs11766101	0.80[EUR][1000 genomes]
rs11768019	0.87[ASN][1000 genomes]
rs11768122	0.85[ASN][1000 genomes]
rs11972895	0.80[EUR][1000 genomes]
rs11975129	0.90[EUR][1000 genomes]
rs11976671	0.80[EUR][1000 genomes]
rs12155372	0.83[EUR][1000 genomes]
rs12670349	0.88[CEU][hapmap]
rs12674340	0.82[EUR][1000 genomes]
rs12701868	0.85[ASN][1000 genomes]
rs12701869	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12701875	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs12701876	0.83[EUR][1000 genomes]
rs12701877	0.83[EUR][1000 genomes]
rs12701879	0.80[EUR][1000 genomes]
rs12701880	0.80[EUR][1000 genomes]
rs13222193	0.88[CEU][hapmap]
rs13222281	0.88[CEU][hapmap]
rs13225532	0.87[ASN][1000 genomes]
rs13230373	0.80[EUR][1000 genomes]
rs13234888	0.88[CEU][hapmap]
rs13238496	0.83[EUR][1000 genomes]
rs13311231	0.87[ASN][1000 genomes]
rs1557931	0.80[EUR][1000 genomes]
rs2189841	0.83[EUR][1000 genomes]
rs255008	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs255009	0.88[EUR][1000 genomes]
rs255010	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs255012	0.87[ASN][1000 genomes]
rs255013	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255014	0.87[ASN][1000 genomes]
rs255015	0.87[ASN][1000 genomes]
rs255016	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255017	0.87[ASN][1000 genomes]
rs255018	0.89[EUR][1000 genomes]
rs29530	0.82[ASN][1000 genomes]
rs29532	0.82[ASN][1000 genomes]
rs29533	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29534	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29535	0.88[EUR][1000 genomes]
rs29536	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29537	0.85[ASN][1000 genomes]
rs29538	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29539	0.85[ASN][1000 genomes]
rs6944817	0.80[EUR][1000 genomes]
rs6951425	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6955172	0.82[EUR][1000 genomes]
rs6974692	0.82[EUR][1000 genomes]
rs756439	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7796964	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs985821	0.83[EUR][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	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534465	chr7:41224437-41443498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10951647	NPC1L1	cis	parietal	SCAN
rs10951647	MYL7	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41234000-41237800	Weak transcription	Brain Substantia Nigra	brain
2	chr7:41236600-41239200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:41236800-41238200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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