Variant report

Variant	rs3774440
Chromosome Location	chr3:53583200-53583201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53577328..53580007-chr3:53582847..53586220,5	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1074235	0.97[ASN][1000 genomes]
rs1547949	0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs17053168	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs33999362	0.88[ASN][1000 genomes]
rs3774428	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774439	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774441	0.96[EUR][1000 genomes]
rs3821846	0.85[CEU][hapmap]
rs3821847	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]
rs59422128	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59512909	0.98[ASN][1000 genomes]
rs62251864	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251869	0.97[ASN][1000 genomes]
rs62251870	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251903	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251904	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6764908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72957281	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740756	0.92[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs9311502	0.83[CEU][hapmap];0.86[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

No data

Chromatin state (count:18 , 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	chr3:53578600-53584200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:53579000-53592000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53580000-53589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:53580200-53584200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:53580400-53587400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:53580600-53584400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:53580800-53583400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:53580800-53584000	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:53580800-53584000	Weak transcription	Fetal Lung	lung
12	chr3:53581400-53583400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:53581400-53587200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:53582600-53583600	Enhancers	Brain Germinal Matrix	brain
15	chr3:53582600-53584000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:53582800-53585200	Weak transcription	Fetal Intestine Large	intestine
17	chr3:53583000-53585800	Weak transcription	Gastric	stomach
18	chr3:53583200-53583400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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