Variant report

Variant	rs3774490
Chromosome Location	chr3:53663648-53663649
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	chr3:53661729..53666678-chr3:53666737..53670217,5	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13059151	0.98[EUR][1000 genomes]
rs13063116	0.87[CEU][hapmap]
rs13084908	0.98[EUR][1000 genomes]
rs1380608	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs17053285	1.00[JPT][hapmap]
rs17053295	1.00[JPT][hapmap]
rs17053338	0.93[GIH][hapmap]
rs17053363	0.93[GIH][hapmap]
rs2292918	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2633709	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2680657	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2680659	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2946522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35768922	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35989759	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36036528	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3774482	0.87[CEU][hapmap]
rs3774483	1.00[JPT][hapmap]
rs3774485	1.00[JPT][hapmap]
rs3774487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774496	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774513	1.00[JPT][hapmap]
rs3821853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66596667	0.98[EUR][1000 genomes]
rs6786894	0.87[CEU][hapmap]
rs6788419	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs71301844	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs898412	1.00[JPT][hapmap]
rs898413	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs898414	1.00[JPT][hapmap]

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	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53652800-53684000	Weak transcription	Right Atrium	heart
2	chr3:53659400-53664600	Weak transcription	Fetal Kidney	kidney
3	chr3:53661400-53667200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:53661600-53665000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53662000-53665400	Enhancers	Stomach Mucosa	stomach
6	chr3:53662200-53663800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53662200-53664000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:53662200-53664200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:53662200-53664800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53662200-53664800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:53662400-53663800	Enhancers	Rectal Smooth Muscle	rectum
12	chr3:53662400-53664400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:53662600-53664200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:53662800-53663800	Enhancers	Colon Smooth Muscle	Colon
15	chr3:53663200-53663800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:53663200-53663800	Enhancers	Esophagus	oesophagus
17	chr3:53663400-53663800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:53663400-53663800	Flanking Active TSS	Lung	lung
19	chr3:53663400-53664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:53663400-53665000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:53663600-53663800	Enhancers	Fetal Brain Female	brain
22	chr3:53663600-53663800	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:53663600-53664000	Weak transcription	Fetal Lung	lung
24	chr3:53663600-53664000	Enhancers	Gastric	stomach
25	chr3:53663600-53664200	Enhancers	Pancreas	Pancrea
26	chr3:53663600-53664600	Weak transcription	HMEC	breast

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