Variant report

Variant	rs13109003
Chromosome Location	chr4:129975969-129975970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10002332	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030831	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037147	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12171333	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13130762	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596963	0.87[ASN][1000 genomes]
rs1699379	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699380	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699384	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699385	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699387	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699388	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699389	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699391	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699393	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699394	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1709419	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1756012	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757924	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757925	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757927	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757928	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757930	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757935	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757936	0.87[AMR][1000 genomes]
rs1854773	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854774	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs189235	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2034498	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2198042	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2597836	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2655310	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280603	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280604	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099899	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105369	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113489	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113490	0.87[AMR][1000 genomes]
rs337263	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs337270	0.95[EUR][1000 genomes]
rs337275	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337277	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337278	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35006492	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389376	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs390260	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs391396	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs395864	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs426521	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4394010	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445294	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4466058	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474667	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs474794	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs487233	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487501	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4975193	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975194	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517659	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57501568	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576492	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58689608	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534707	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66921209	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655841	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671508	0.87[AMR][1000 genomes]
rs789982	0.87[AMR][1000 genomes]

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	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	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13109003	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs13109003	C4orf33	cis	Artery Tibial	GTEx
rs13109003	C4orf33	cis	Whole Blood	GTEx
rs13109003	C4orf33	cis	multi-tissue	Pritchard
rs13109003	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs13109003	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
2	chr4:129951400-129976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:129974400-129976400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:129975600-129977400	ZNF genes & repeats	Fetal Lung	lung

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