Variant report

Variant	rs876538
Chromosome Location	chr1:159675717-159675718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11591079	1.00[CHB][hapmap]
rs17427209	1.00[CHB][hapmap]
rs17467492	1.00[CHB][hapmap]
rs2808627	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2808634	0.98[AFR][1000 genomes]
rs3116650	0.98[AFR][1000 genomes]
rs3116652	0.98[AFR][1000 genomes]
rs4420078	0.86[YRI][hapmap]
rs4425982	0.85[AFR][1000 genomes]
rs6662675	1.00[CHB][hapmap]
rs6662918	1.00[CHB][hapmap]

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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	90 gene(s)	inside rSNPs	diseases
2	esv1816835	chr1:159635021-159678816	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1829893	chr1:159635021-159678816	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv3188	chr1:159635132-159676182	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs876538	PPOX	cis	cerebellum	SCAN
rs876538	FDPS	cis	parietal	SCAN
rs876538	DAAM1	trans	cerebellum	SCAN
rs876538	B4GALT3	cis	parietal	SCAN
rs876538	PMVK	cis	parietal	SCAN
rs876538	DCAF8	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159669800-159682000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:159674400-159676000	Enhancers	Brain Hippocampus Middle	brain
3	chr1:159674400-159676200	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:159674600-159676000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:159674600-159676000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:159674600-159676000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr1:159674600-159676000	Enhancers	Brain Substantia Nigra	brain
8	chr1:159674600-159678600	Enhancers	Liver	Liver
9	chr1:159674800-159675800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:159675000-159676000	Enhancers	Brain Angular Gyrus	brain
11	chr1:159675200-159678200	Enhancers	Fetal Intestine Small	intestine
12	chr1:159675400-159675800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:159675600-159676000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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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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