Variant report

Variant	rs2735839
Chromosome Location	chr19:51364623-51364624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1058205	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174776	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1810020	0.95[ASN][1000 genomes]
rs2569735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659122	0.80[CHD][hapmap]
rs2659124	0.86[ASN][1000 genomes]
rs266878	0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][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	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv2531	chr19:51333628-51378597	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2763208	chr19:51361757-51377163	ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Prostate-specific antigen levels	23269536	GWAS catalog
Prostate cancer	18264097	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2735839	CNOT3	cis	cerebellum	SCAN
rs2735839	ZNF444	cis	parietal	SCAN
rs2735839	KIR3DX1	cis	cerebellum	SCAN
rs2735839	RIT1	trans	lymphoblastoid	seeQTL
rs2735839	SIGLEC5	cis	parietal	SCAN
rs2735839	LILRA5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51361400-51364800	Enhancers	Esophagus	oesophagus
2	chr19:51364600-51364800	Weak transcription	Pancreas	Pancrea
3	chr19:51364600-51365000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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