Variant report

Variant	rs939442
Chromosome Location	chr3:180038381-180038382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr3:180038277-180038475	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000239880	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10755138	0.85[ASN][1000 genomes]
rs10937030	0.86[ASN][1000 genomes]
rs12486206	0.96[ASN][1000 genomes]
rs12491089	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497420	0.90[ASN][1000 genomes]
rs12638851	0.94[ASN][1000 genomes]
rs12638877	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464358	0.86[ASN][1000 genomes]
rs1520613	0.83[ASN][1000 genomes]
rs16831288	0.81[ASN][1000 genomes]
rs16831406	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2337367	0.85[ASN][1000 genomes]
rs2337368	0.81[ASN][1000 genomes]
rs2337369	0.84[ASN][1000 genomes]
rs2878951	0.86[ASN][1000 genomes]
rs2878954	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3849424	0.84[ASN][1000 genomes]
rs3849425	0.84[ASN][1000 genomes]
rs3849426	0.84[ASN][1000 genomes]
rs3906013	0.82[ASN][1000 genomes]
rs3906014	0.81[ASN][1000 genomes]
rs3914867	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3914868	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3914869	0.84[ASN][1000 genomes]
rs3914871	0.84[ASN][1000 genomes]
rs4241377	0.83[ASN][1000 genomes]
rs4568133	0.84[ASN][1000 genomes]
rs4854969	0.83[ASN][1000 genomes]
rs4854970	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55996463	0.84[ASN][1000 genomes]
rs62292326	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769259	0.84[ASN][1000 genomes]
rs7622125	0.82[ASN][1000 genomes]
rs7622865	0.81[ASN][1000 genomes]
rs7636890	0.87[ASN][1000 genomes]
rs7639931	0.83[ASN][1000 genomes]
rs7643438	0.85[ASN][1000 genomes]
rs7644566	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652473	0.82[ASN][1000 genomes]
rs939440	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939441	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9682110	0.84[ASN][1000 genomes]
rs9683358	0.97[ASN][1000 genomes]
rs9713189	0.86[ASN][1000 genomes]
rs9713891	0.86[ASN][1000 genomes]
rs9818172	0.83[ASN][1000 genomes]
rs9819178	0.82[ASN][1000 genomes]
rs9824544	0.82[ASN][1000 genomes]
rs9860910	0.85[ASN][1000 genomes]
rs9864534	0.85[ASN][1000 genomes]
rs9867767	0.96[ASN][1000 genomes]
rs9869873	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs939442	ARFGAP1	trans	cerebellum	SCAN
rs939442	ABCC5	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180024800-180039000	Weak transcription	Ovary	ovary
2	chr3:180037000-180038400	Enhancers	Osteobl	bone
3	chr3:180037000-180038600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr3:180037000-180038800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:180037200-180039000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:180037400-180039000	Enhancers	HMEC	breast
7	chr3:180038200-180038800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:180038200-180038800	Enhancers	NHLF	lung

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