Variant report

Variant	rs3821847
Chromosome Location	chr3:53587277-53587278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53583822..53587338-chr3:53599024..53602468,3	MCF-7	breast:
2	chr3:53586030..53587817-chr3:53589041..53592025,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1074235	0.98[ASN][1000 genomes]
rs1547949	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs17053168	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs33999362	0.83[ASN][1000 genomes]
rs3774428	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774439	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774441	0.92[EUR][1000 genomes]
rs3774558	1.00[LWK][hapmap]
rs3821846	0.85[CEU][hapmap]
rs59422128	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59512909	0.94[ASN][1000 genomes]
rs62251864	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62251868	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251869	0.98[ASN][1000 genomes]
rs62251870	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62251903	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62251904	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72957281	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs740756	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9311502	0.83[CEU][hapmap];0.81[TSI][hapmap];0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3821847	DCP1A	cis	parietal	SCAN
rs3821847	SPCS1	cis	parietal	SCAN
rs3821847	GNL3	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr3:53580400-53587400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:53584800-53592600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:53586200-53587600	Weak transcription	GM12878-XiMat	blood
6	chr3:53586200-53600800	Weak transcription	Fetal Intestine Large	intestine
7	chr3:53586400-53587400	Weak transcription	Gastric	stomach
8	chr3:53586400-53587800	Enhancers	Fetal Intestine Small	intestine
9	chr3:53586600-53587600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:53586600-53589800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:53587000-53587400	Enhancers	Duodenum Mucosa	Duodenum
12	chr3:53587000-53587600	Enhancers	Stomach Smooth Muscle	stomach
13	chr3:53587000-53587800	Enhancers	Fetal Lung	lung
14	chr3:53587200-53587600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53587200-53587600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:53587200-53587600	Enhancers	Fetal Brain Male	brain
17	chr3:53587200-53587600	Enhancers	Pancreas	Pancrea
18	chr3:53587200-53587800	Enhancers	Fetal Brain Female	brain
19	chr3:53587200-53587800	Enhancers	Fetal Kidney	kidney

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