Variant report

Variant	rs474667
Chromosome Location	chr4:130038714-130038715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10002332	0.89[EUR][1000 genomes]
rs1030831	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1037147	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12171333	0.89[EUR][1000 genomes]
rs13109003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13130762	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1374491	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1699379	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699380	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1699384	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699385	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1699387	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699388	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1699389	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1699391	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1699393	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1699394	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17014265	0.80[ASN][1000 genomes]
rs1709419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1756012	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757924	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757925	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757927	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757928	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757930	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757935	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1854773	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs189235	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034498	0.86[EUR][1000 genomes]
rs2198042	0.91[EUR][1000 genomes]
rs2597836	0.84[EUR][1000 genomes]
rs2655310	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs280603	0.91[EUR][1000 genomes]
rs280604	0.89[EUR][1000 genomes]
rs3099899	0.91[EUR][1000 genomes]
rs3105369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3113489	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs337263	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337270	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337275	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337277	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337278	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35006492	0.89[EUR][1000 genomes]
rs389376	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390260	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391396	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395864	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs426521	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394010	0.89[EUR][1000 genomes]
rs445294	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4466058	0.91[EUR][1000 genomes]
rs474794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487233	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs487501	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975193	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4975194	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs517659	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57501568	0.90[EUR][1000 genomes]
rs576492	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58689608	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6534707	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66921209	0.87[EUR][1000 genomes]
rs7655841	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs474667	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs474667	C4orf33	cis	Artery Tibial	GTEx
rs474667	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs474667	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs474667	C4orf33	cis	Adipose Subcutaneous	GTEx
rs474667	C4orf33	cis	Whole Blood	GTEx
rs474667	C4orf33	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130040400	Weak transcription	Lung	lung
2	chr4:130029200-130040000	Weak transcription	Esophagus	oesophagus
3	chr4:130029400-130041200	Weak transcription	Spleen	Spleen
4	chr4:130031800-130039800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:130031800-130040000	Weak transcription	Dnd41	blood
6	chr4:130032400-130040000	Weak transcription	Primary T cells from cord blood	blood
7	chr4:130032400-130052200	Weak transcription	Aorta	Aorta
8	chr4:130036000-130044600	Weak transcription	Pancreas	Pancrea
9	chr4:130038600-130039400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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