Variant report

Variant	rs9840954
Chromosome Location	chr3:145952718-145952719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1061409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13079270	0.87[YRI][hapmap]
rs13326891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398526	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398528	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398530	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512889	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2175669	0.87[YRI][hapmap]
rs28419536	0.81[EUR][1000 genomes]
rs35418885	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804647	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804649	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4314144	0.88[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681115	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57294001	0.80[ASN][1000 genomes]
rs57764107	0.92[ASN][1000 genomes]
rs59965250	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792036	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792166	0.92[ASN][1000 genomes]
rs6792604	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804987	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611293	0.93[ASN][1000 genomes]
rs7611299	0.91[ASN][1000 genomes]
rs7611459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611582	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633567	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809574	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814972	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9821768	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9830885	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9838816	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844172	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850144	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854377	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854697	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870547	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870686	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870699	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874072	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874112	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874234	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876826	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876833	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880432	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3452197	chr3:145950303-145974111	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840954	PLSCR4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:145940600-145953000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:145940600-145953600	Weak transcription	NHDF-Ad	bronchial
4	chr3:145941600-145954000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:145942200-145953400	Weak transcription	HUVEC	blood vessel
6	chr3:145945200-145959800	Weak transcription	Ovary	ovary
7	chr3:145946400-145953000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:145947200-145953000	Weak transcription	Adipose Nuclei	Adipose
9	chr3:145947400-145953200	Weak transcription	Fetal Intestine Large	intestine
10	chr3:145948000-145967800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:145950800-145953000	Weak transcription	Fetal Lung	lung
12	chr3:145951000-145953000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:145952200-145953000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:145952400-145953000	Weak transcription	Aorta	Aorta
15	chr3:145952400-145953200	ZNF genes & repeats	Fetal Stomach	stomach
16	chr3:145952600-145954400	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr3:145952600-145955000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:145952600-145956200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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