Variant report

Variant	rs2796843
Chromosome Location	chr13:51240182-51240183
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12853944	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2794460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794467	0.93[ASN][1000 genomes]
rs3095526	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3116599	1.00[ASW][hapmap]
rs3116618	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3116620	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3121210	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3121212	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[MKK][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs637310	0.85[AMR][1000 genomes];0.82[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	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
2	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2796843	STAT2	trans	brain	seeQTL
rs2796843	DDX39A	trans	brain	seeQTL
rs2796843	LSS	trans	brain	seeQTL
rs2796843	PLIN3	trans	brain	seeQTL
rs2796843	IFITM1	trans	brain	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51237200-51240800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr13:51237400-51245200	Weak transcription	Osteobl	bone
3	chr13:51239400-51241000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:51239800-51241000	ZNF genes & repeats	Thymus	Thymus
5	chr13:51240000-51240200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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