Variant report

Variant	rs3774421
Chromosome Location	chr3:53551010-53551011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17788662	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774419	0.86[TSI][hapmap]
rs3774424	0.92[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62251862	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3434928	chr3:53550812-53554010	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3774421	GNL3	cis	cerebellum	SCAN
rs3774421	ITIH3	cis	parietal	SCAN
rs3774421	DCP1A	cis	parietal	SCAN
rs3774421	SPCS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53533600-53552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:53540600-53552200	Weak transcription	Spleen	Spleen
3	chr3:53540600-53560000	Weak transcription	Pancreas	Pancrea
4	chr3:53542600-53551400	Strong transcription	Fetal Intestine Large	intestine
5	chr3:53545200-53552800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53545400-53552800	Weak transcription	Fetal Stomach	stomach
7	chr3:53545600-53551200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:53545600-53552000	Weak transcription	Lung	lung
9	chr3:53547200-53553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53548200-53552200	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53550000-53552000	Enhancers	A549	lung
12	chr3:53550600-53551400	Strong transcription	Fetal Lung	lung
13	chr3:53550800-53552000	Enhancers	Hela-S3	cervix

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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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