Variant report

Variant	rs12701869
Chromosome Location	chr7:41254747-41254748
allele	C/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:39)

rs_ID	r²[population]
rs10214990	0.80[EUR][1000 genomes]
rs10225564	0.80[EUR][1000 genomes]
rs10233411	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242681	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs10281338	0.80[EUR][1000 genomes]
rs10951647	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10951648	0.81[EUR][1000 genomes]
rs11760865	0.80[EUR][1000 genomes]
rs11768019	0.86[ASN][1000 genomes]
rs11768122	0.86[ASN][1000 genomes]
rs12155372	0.81[EUR][1000 genomes]
rs12674340	0.80[EUR][1000 genomes]
rs12701868	0.86[ASN][1000 genomes]
rs12701870	0.88[ASN][1000 genomes]
rs12701875	0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs12701876	0.81[EUR][1000 genomes]
rs12701877	0.81[EUR][1000 genomes]
rs13238496	0.81[EUR][1000 genomes]
rs13244372	0.82[ASN][1000 genomes]
rs13311231	0.86[ASN][1000 genomes]
rs2051869	0.82[ASN][1000 genomes]
rs2051871	0.82[ASN][1000 genomes]
rs2189841	0.83[EUR][1000 genomes]
rs255008	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs255010	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs255013	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs255016	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29533	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29534	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29536	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29538	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34965184	0.82[ASN][1000 genomes]
rs56215033	0.87[ASN][1000 genomes]
rs6951425	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs6951590	0.80[EUR][1000 genomes]
rs756439	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782143	0.85[ASN][1000 genomes]
rs7796964	0.81[EUR][1000 genomes]
rs985821	0.81[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
rs12701869	NPC1L1	cis	parietal	SCAN
rs12701869	MYL7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41246200-41257000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:41254200-41256000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:41254600-41258600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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