Variant report

Variant	rs3774488
Chromosome Location	chr3:53662280-53662281
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: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13059151	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13063116	0.87[CEU][hapmap]
rs13084908	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2292918	0.84[CHB][hapmap]
rs2633709	1.00[JPT][hapmap]
rs2680657	0.84[CHB][hapmap]
rs2680659	0.85[CHB][hapmap]
rs2946522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35768922	0.98[EUR][1000 genomes]
rs35989759	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36036528	0.98[EUR][1000 genomes]
rs3774487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774490	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];0.96[ASN][1000 genomes]
rs3774503	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]
rs3821853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66596667	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6786894	0.87[CEU][hapmap]
rs6788419	1.00[JPT][hapmap]
rs71301844	0.98[EUR][1000 genomes]
rs898413	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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53652800-53684000	Weak transcription	Right Atrium	heart
2	chr3:53659000-53662400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53659000-53662800	Weak transcription	Fetal Brain Male	brain
4	chr3:53659200-53663400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:53659400-53664600	Weak transcription	Fetal Kidney	kidney
6	chr3:53659600-53662800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:53659600-53662800	Weak transcription	Fetal Brain Female	brain
8	chr3:53659600-53663400	Weak transcription	Lung	lung
9	chr3:53659600-53663600	Weak transcription	Pancreas	Pancrea
10	chr3:53660200-53662600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:53661400-53667200	Weak transcription	Fetal Intestine Large	intestine
12	chr3:53661600-53663200	Weak transcription	Esophagus	oesophagus
13	chr3:53661600-53665000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:53662000-53663600	Enhancers	Fetal Lung	lung
15	chr3:53662000-53665400	Enhancers	Stomach Mucosa	stomach
16	chr3:53662200-53662800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:53662200-53662800	Enhancers	Stomach Smooth Muscle	stomach
18	chr3:53662200-53663600	Enhancers	HMEC	breast
19	chr3:53662200-53663800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:53662200-53664000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:53662200-53664200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:53662200-53664800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:53662200-53664800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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