Variant report

Variant	rs7138703
Chromosome Location	chr12:47340921-47340922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10785646	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10881009	0.86[EUR][1000 genomes]
rs10881011	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881013	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183625	0.80[CHB][hapmap]
rs11183661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183665	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183666	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183671	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183672	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11609950	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12229470	0.85[EUR][1000 genomes]
rs12423364	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1986584	0.86[EUR][1000 genomes]
rs2250595	0.80[EUR][1000 genomes]
rs2253630	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465221	0.86[EUR][1000 genomes]
rs2465222	0.86[EUR][1000 genomes]
rs2465223	0.86[EUR][1000 genomes]
rs2465227	0.86[EUR][1000 genomes]
rs2465228	0.86[EUR][1000 genomes]
rs2465229	0.83[EUR][1000 genomes]
rs2465230	0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2465232	0.83[EUR][1000 genomes]
rs2465597	0.83[EUR][1000 genomes]
rs2465617	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2465627	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465628	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465630	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4374015	0.80[CHB][hapmap]
rs4405401	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4586261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582686	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137808	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295618	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7962539	0.81[EUR][1000 genomes]
rs7963326	0.86[EUR][1000 genomes]
rs7966987	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7975211	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7138703	CCNT1	cis	parietal	SCAN
rs7138703	RAPGEF3	cis	cerebellum	SCAN
rs7138703	PFKM	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47335800-47343400	Enhancers	NHDF-Ad	bronchial
2	chr12:47337000-47350400	Weak transcription	Psoas Muscle	Psoas
3	chr12:47337200-47342400	Weak transcription	Hela-S3	cervix
4	chr12:47337600-47342400	Weak transcription	NHLF	lung
5	chr12:47338200-47343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:47338400-47343800	Weak transcription	HMEC	breast
7	chr12:47338400-47343800	Weak transcription	NHEK	skin
8	chr12:47338800-47349800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:47339000-47342400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:47339400-47341200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:47340000-47341000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:47340800-47341000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:47340800-47341000	ZNF genes & repeats	Pancreas	Pancrea
14	chr12:47340800-47341200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:47340800-47342600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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