Variant report

Variant	rs4802135
Chromosome Location	chr19:38346712-38346713
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10401637	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10401968	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10402530	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404567	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10409402	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10409487	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10420746	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10420891	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427125	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11878269	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879180	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1291	0.86[CHB][hapmap]
rs12974225	0.85[CHB][hapmap]
rs12975057	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979640	0.86[CHB][hapmap]
rs1643466	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs1643467	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1643468	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs171376	0.81[EUR][1000 genomes]
rs1725481	0.80[JPT][hapmap]
rs2068431	0.85[ASN][1000 genomes]
rs2075281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287229	0.86[CHB][hapmap]
rs241932	0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs241950	0.81[EUR][1000 genomes]
rs2909088	0.86[CHB][hapmap]
rs2909093	0.86[CHB][hapmap]
rs2909098	0.85[CHB][hapmap]
rs2909102	0.86[CHB][hapmap]
rs2909105	0.86[CHB][hapmap]
rs2909109	0.86[CHB][hapmap]
rs2927739	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2927747	0.86[CHB][hapmap]
rs2972437	0.86[CHB][hapmap]
rs2972438	0.86[CHB][hapmap]
rs2972439	0.86[CHB][hapmap]
rs2972448	0.86[CHB][hapmap]
rs3095726	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs35209753	0.86[EUR][1000 genomes]
rs353414	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs353423	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3848626	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910952	0.81[ASN][1000 genomes]
rs4803509	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4803524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803528	0.85[ASN][1000 genomes]
rs58449039	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508742	0.85[EUR][1000 genomes]
rs705492	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs705494	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs7245864	0.84[ASN][1000 genomes]
rs7250409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7250571	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250868	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252010	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257125	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7258597	0.84[EUR][1000 genomes]
rs8101752	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101858	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104076	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110284	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs8112706	0.86[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs8182498	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833895	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs833914	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs856300	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs856304	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs9304569	0.85[EUR][1000 genomes]
rs9304572	0.82[EUR][1000 genomes]
rs968073	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3434717	chr19:38326161-38347208	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1832898	chr19:38341754-38362792	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1825275	chr19:38341754-38376485	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	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
rs4802135	ZNF571	cis	multi-tissue	Pritchard
rs4802135	WDR87	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38345200-38347200	ZNF genes & repeats	Esophagus	oesophagus
2	chr19:38345400-38347200	ZNF genes & repeats	Placenta	Placenta
3	chr19:38345400-38347600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:38345600-38347000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
5	chr19:38345600-38347000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:38345600-38347000	ZNF genes & repeats	Spleen	Spleen
7	chr19:38345600-38347200	ZNF genes & repeats	Pancreas	Pancrea
8	chr19:38345600-38347200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:38345600-38347400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:38345600-38347400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:38345800-38346800	Enhancers	Fetal Brain Male	brain
12	chr19:38345800-38346800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
13	chr19:38345800-38347200	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr19:38346000-38346800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:38346600-38346800	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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