Variant report

Variant	rs1093330
Chromosome Location	chr12:117696534-117696535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10774910	0.83[GIH][hapmap]
rs1093328	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1093329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682819	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2682820	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682821	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682822	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741476	0.83[GIH][hapmap]
rs7959232	0.85[GIH][hapmap]
rs816348	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs816353	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816355	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816356	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816359	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs816363	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs845820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs904658	0.83[GIH][hapmap]
rs939474	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9658498	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1051681	chr12:117692761-117720185	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1093330	RNFT2	cis	parietal	SCAN
rs1093330	RASAL1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117660000-117727400	Weak transcription	Psoas Muscle	Psoas
2	chr12:117666200-117704200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117674800-117706600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:117691000-117697400	Strong transcription	NHEK	skin
5	chr12:117693800-117698200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:117693800-117715200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:117695600-117718200	Weak transcription	Pancreas	Pancrea
8	chr12:117695800-117697000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:117696000-117697200	Strong transcription	Brain Anterior Caudate	brain
10	chr12:117696000-117698200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:117696000-117698400	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:117696400-117698400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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