Variant report

Variant	rs991818
Chromosome Location	chr3:53587519-53587520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12629517	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap]
rs13078747	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs17053168	0.83[YRI][hapmap]
rs34106488	0.83[ASN][1000 genomes]
rs35131285	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774426	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6777870	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs991818	NT5DC2	cis	parietal	SCAN
rs991818	GNAT1	cis	parietal	SCAN
rs991818	DCP1A	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53579000-53592000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:53580000-53589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:53584800-53592600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:53586200-53587600	Weak transcription	GM12878-XiMat	blood
5	chr3:53586200-53600800	Weak transcription	Fetal Intestine Large	intestine
6	chr3:53586400-53587800	Enhancers	Fetal Intestine Small	intestine
7	chr3:53586600-53587600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:53586600-53589800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:53587000-53587600	Enhancers	Stomach Smooth Muscle	stomach
10	chr3:53587000-53587800	Enhancers	Fetal Lung	lung
11	chr3:53587200-53587600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:53587200-53587600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:53587200-53587600	Enhancers	Fetal Brain Male	brain
14	chr3:53587200-53587600	Enhancers	Pancreas	Pancrea
15	chr3:53587200-53587800	Enhancers	Fetal Brain Female	brain
16	chr3:53587200-53587800	Enhancers	Fetal Kidney	kidney
17	chr3:53587400-53587600	Enhancers	Gastric	stomach
18	chr3:53587400-53587800	Enhancers	Rectal Smooth Muscle	rectum

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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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