Variant report

Variant	rs9562736
Chromosome Location	chr13:47995252-47995253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs7324949	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567857	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567859	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9567864	0.88[ASN][1000 genomes]
rs9567867	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763019	chr13:47348229-48123447	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3394678	chr13:47678184-48039379	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3450125	chr13:47919050-48236684	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv455879	chr13:47919611-48190106	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv561588	chr13:47943829-48190106	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9562736	C13orf31	cis	cerebellum	SCAN
rs9562736	CCDC122	cis	cerebellum	SCAN
rs9562736	LCP1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:47993200-47995600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr13:47993200-47996400	Enhancers	NHDF-Ad	bronchial
3	chr13:47993400-47997000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:47994200-47995800	Enhancers	Liver	Liver
5	chr13:47994200-47996400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr13:47994800-47995800	Enhancers	Adipose Nuclei	Adipose
7	chr13:47995000-47995600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr13:47995000-48000200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr13:47995000-48000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:47995200-47995600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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Input of quick search could be:

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

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