Variant report

Variant	rs17338729
Chromosome Location	chr3:100629651-100629652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10049238	1.00[JPT][hapmap]
rs1036468	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10511180	1.00[JPT][hapmap]
rs12330346	1.00[JPT][hapmap]
rs1375510	1.00[JPT][hapmap]
rs1449321	1.00[JPT][hapmap]
rs17339226	0.88[CHB][hapmap]
rs17398137	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs1821795	1.00[JPT][hapmap]
rs1836985	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2245370	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2252229	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs2304513	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs2576367	1.00[JPT][hapmap]
rs2576370	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs2576384	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs2576385	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2576389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576390	1.00[JPT][hapmap]
rs2595899	1.00[JPT][hapmap]
rs2713749	0.88[CHB][hapmap]
rs2713750	1.00[JPT][hapmap]
rs2713759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2713762	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2713794	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs28605965	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6774218	0.88[CHB][hapmap]
rs73143029	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355920	0.81[ASW][hapmap];1.00[JPT][hapmap]
rs7609734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7625454	0.88[CHB][hapmap]
rs7641631	0.88[CHB][hapmap]
rs7646218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7647099	1.00[JPT][hapmap]
rs7651634	1.00[JPT][hapmap]
rs9653904	1.00[JPT][hapmap]
rs9822089	1.00[JPT][hapmap]
rs9824648	1.00[JPT][hapmap]
rs9825288	1.00[JPT][hapmap]
rs9826284	1.00[JPT][hapmap]
rs9827075	1.00[JPT][hapmap]
rs9827694	1.00[JPT][hapmap]
rs9831620	1.00[JPT][hapmap]
rs9843102	1.00[JPT][hapmap]
rs9844950	0.81[ASW][hapmap];1.00[JPT][hapmap]
rs9847485	1.00[JPT][hapmap]
rs9860250	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs9862373	1.00[JPT][hapmap]
rs9866199	1.00[JPT][hapmap]
rs9881388	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17338729	CPOX	cis	cerebellum	SCAN
rs17338729	JAKMIP2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
3	chr3:100617600-100641000	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:100617800-100641000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:100621600-100633400	Weak transcription	HSMMtube	muscle
6	chr3:100622000-100631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:100623200-100631800	Weak transcription	NHDF-Ad	bronchial
8	chr3:100623600-100629800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:100629000-100630000	Weak transcription	NHLF	lung
10	chr3:100629400-100629800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:100629600-100630000	Weak transcription	Ovary	ovary
12	chr3:100629600-100630400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:100629600-100630400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:100629600-100630400	Enhancers	Osteobl	bone
15	chr3:100629600-100630600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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