Variant report

Variant	rs3774439
Chromosome Location	chr3:53581725-53581726
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10049492	0.87[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17053168	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3774425	0.86[GIH][hapmap]
rs3774428	0.83[CEU][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3774440	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774441	0.97[EUR][1000 genomes]
rs3821846	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs3821847	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59422128	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62251864	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62251868	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62251870	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62251903	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62251904	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62251905	0.86[ASN][1000 genomes]
rs6764908	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72957281	0.88[EUR][1000 genomes]
rs807190	0.87[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9311502	0.83[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3774439	NT5DC2	cis	parietal	SCAN
rs3774439	GNL3	cis	cerebellum	SCAN
rs3774439	SPCS1	cis	parietal	SCAN
rs3774439	DCP1A	cis	parietal	SCAN
rs3774439	CACNA2D2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53560600-53587000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53566400-53583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:53569400-53581800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:53569600-53581800	Weak transcription	Fetal Intestine Large	intestine
5	chr3:53578600-53584200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:53579000-53592000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53580000-53589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:53580200-53584200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:53580400-53587400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:53580600-53584400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:53580800-53583400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:53580800-53584000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:53580800-53584000	Weak transcription	Fetal Lung	lung
14	chr3:53581200-53582600	Strong transcription	Fetal Intestine Small	intestine
15	chr3:53581400-53583400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:53581400-53587200	Weak transcription	H9 Derived Neuronal Progenitor 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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