Variant report

Variant	rs4405401
Chromosome Location	chr12:47336015-47336016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10785646	0.89[EUR][1000 genomes]
rs10881009	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10881011	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10881013	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183625	0.80[CHB][hapmap]
rs11183644	0.85[AFR][1000 genomes]
rs11183661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183665	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183666	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183671	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183672	0.89[EUR][1000 genomes]
rs11609950	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12229470	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12423364	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17684703	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1986584	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2250595	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2253630	0.82[EUR][1000 genomes]
rs2465617	0.90[ASN][1000 genomes]
rs2465627	0.82[EUR][1000 genomes]
rs2465628	0.82[EUR][1000 genomes]
rs2465630	0.82[EUR][1000 genomes]
rs4374015	0.80[CHB][hapmap]
rs4586261	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582686	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137439	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7137808	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138703	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295618	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962539	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963326	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7966987	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972871	0.80[AFR][1000 genomes]
rs7975211	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978950	0.95[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4405401	PFKM	cis	cerebellum	SCAN
rs4405401	CCNT1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47332400-47336200	Weak transcription	NH-A	brain
2	chr12:47332400-47337600	Weak transcription	A549	lung
3	chr12:47332800-47336600	Weak transcription	Liver	Liver
4	chr12:47332800-47338000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:47335400-47338800	Enhancers	HSMM	muscle
6	chr12:47335400-47339000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:47335600-47336600	Weak transcription	HSMMtube	muscle
8	chr12:47335600-47337200	Enhancers	Hela-S3	cervix
9	chr12:47335600-47337400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:47335600-47337400	Enhancers	HMEC	breast
11	chr12:47335600-47337600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:47335600-47338400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:47335600-47338400	Enhancers	NHEK	skin
14	chr12:47335800-47337000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:47335800-47337000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:47335800-47337000	Enhancers	Psoas Muscle	Psoas
17	chr12:47335800-47337200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:47335800-47337200	Enhancers	HUVEC	blood vessel
19	chr12:47335800-47338200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:47335800-47338200	Enhancers	Osteobl	bone
21	chr12:47335800-47339400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:47335800-47343400	Enhancers	NHDF-Ad	bronchial
23	chr12:47336000-47336800	Weak transcription	NHLF	lung
24	chr12:47336000-47338400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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