Variant report

Variant	rs7314477
Chromosome Location	chr12:41296854-41296855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1028949	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11178978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12301044	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12367345	0.85[MEX][hapmap]
rs12578583	0.83[ASN][1000 genomes]
rs12578762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579682	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580909	0.83[ASN][1000 genomes]
rs12581257	0.83[ASN][1000 genomes]
rs12581462	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12582450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582480	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12582790	0.83[ASN][1000 genomes]
rs12582806	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12810195	0.83[ASN][1000 genomes]
rs12824161	0.83[ASN][1000 genomes]
rs34409157	0.83[ASN][1000 genomes]
rs34435345	0.83[ASN][1000 genomes]
rs34480545	0.97[ASN][1000 genomes]
rs34588792	0.83[ASN][1000 genomes]
rs35067046	0.83[ASN][1000 genomes]
rs35640051	0.83[ASN][1000 genomes]
rs35840550	0.83[ASN][1000 genomes]
rs56928815	0.83[ASN][1000 genomes]
rs59969287	0.83[ASN][1000 genomes]
rs7303594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307211	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310770	0.83[ASN][1000 genomes]
rs7311456	0.83[ASN][1000 genomes]
rs73118754	0.83[ASN][1000 genomes]
rs73118756	0.83[ASN][1000 genomes]
rs7312428	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960431	0.86[ASN][1000 genomes]
rs7969238	0.80[EUR][1000 genomes];0.92[ASN][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	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7314477	VTN	trans	parietal	SCAN
rs7314477	CNTN1	cis	cerebellum	SCAN
rs7314477	KIF21A	cis	cerebellum	SCAN
rs7314477	ZNF793	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41285000-41304600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:41294800-41297000	Weak transcription	Ovary	ovary
3	chr12:41296000-41297200	Enhancers	A549	lung
4	chr12:41296600-41297600	Enhancers	NHEK	skin
5	chr12:41296800-41297200	Enhancers	HMEC	breast
6	chr12:41296800-41297400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:41296800-41297400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:41296800-41297400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr12:41296800-41297600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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