Variant report

Variant	rs11086852
Chromosome Location	chr20:41420166-41420167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10470022	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs11696719	0.85[CEU][hapmap]
rs11698772	0.85[CEU][hapmap]
rs16987367	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16987425	0.85[CEU][hapmap]
rs4812634	1.00[CHB][hapmap]
rs6016891	1.00[JPT][hapmap]
rs6030465	1.00[JPT][hapmap]
rs6030467	0.85[CEU][hapmap]
rs62205408	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7261303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7261359	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7265982	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7268984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7273962	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs73269898	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962251	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

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	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11086852	CD40	cis	parietal	SCAN
rs11086852	WFDC13	cis	cerebellum	SCAN
rs11086852	OR8D2	trans	parietal	SCAN
rs11086852	CHD6	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41407400-41420800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:41414400-41420800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:41416200-41420200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr20:41416200-41421400	Weak transcription	Brain Anterior Caudate	brain
5	chr20:41417000-41424200	Weak transcription	Pancreas	Pancrea
6	chr20:41419600-41421800	Enhancers	Brain Substantia Nigra	brain
7	chr20:41420000-41421800	Enhancers	Brain Hippocampus Middle	brain
8	chr20:41420000-41421800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr20:41420000-41437600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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