Variant report

Variant	rs3821846
Chromosome Location	chr3:53585307-53585308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53557133..53558242-chr3:53585061..53585903,3	MCF-7	breast:
2	chr3:53584851..53587077-chr3:53602555..53604461,2	MCF-7	breast:
3	chr3:53577328..53580007-chr3:53582847..53586220,5	MCF-7	breast:
4	chr3:53585012..53585627-chr3:53741687..53742458,2	MCF-7	breast:
5	chr3:53552367..53553946-chr3:53584985..53585902,8	MCF-7	breast:
6	chr3:53552361..53553110-chr3:53585085..53585894,4	MCF-7	breast:
7	chr3:53179051..53179721-chr3:53585086..53585781,2	MCF-7	breast:
8	chr3:53552476..53553069-chr3:53585002..53585791,2	MCF-7	breast:
9	chr3:53553135..53554029-chr3:53584915..53585873,10	MCF-7	breast:
10	chr3:53553135..53553983-chr3:53584999..53585589,3	MCF-7	breast:
11	chr3:53583822..53587338-chr3:53599024..53602468,3	MCF-7	breast:
12	chr3:53584684..53586821-chr3:53697849..53700213,2	MCF-7	breast:
13	chr3:53584946..53585871-chr3:53698734..53699592,4	MCF-7	breast:
14	chr3:53552361..53552892-chr3:53585085..53585894,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10049492	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs1074235	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1547949	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs1547951	0.89[EUR][1000 genomes]
rs17053168	0.84[CEU][hapmap]
rs3774439	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]
rs3774440	0.85[CEU][hapmap]
rs3821847	0.85[CEU][hapmap]
rs55828852	0.95[EUR][1000 genomes]
rs59512909	0.95[EUR][1000 genomes]
rs62251869	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62251905	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6764908	0.85[CEU][hapmap]
rs740756	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs807190	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9311502	0.88[GIH][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3821846	DCP1A	cis	parietal	SCAN
rs3821846	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	chr3:53579000-53592000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53580000-53589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:53580400-53587400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:53581400-53587200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53583000-53585800	Weak transcription	Gastric	stomach
7	chr3:53583400-53586200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:53584000-53585600	Strong transcription	Fetal Intestine Small	intestine
9	chr3:53584000-53586400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:53584400-53585600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:53584400-53587200	Weak transcription	Pancreas	Pancrea
12	chr3:53584600-53585400	Weak transcription	Lung	lung
13	chr3:53584600-53587000	Weak transcription	Fetal Lung	lung
14	chr3:53584600-53587200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:53584800-53592600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:53585200-53586200	Enhancers	Fetal Intestine Large	intestine

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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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