Variant report

Variant	rs72976490
Chromosome Location	chr3:53663699-53663700
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: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1356657	1.00[AMR][1000 genomes]
rs1356658	1.00[AMR][1000 genomes]
rs1401493	1.00[AMR][1000 genomes]
rs1401498	1.00[AMR][1000 genomes]
rs2612017	1.00[AMR][1000 genomes]
rs2612021	1.00[AMR][1000 genomes]
rs2633711	1.00[AMR][1000 genomes]
rs2633712	1.00[AMR][1000 genomes]
rs2633733	1.00[AMR][1000 genomes]
rs2680653	1.00[AMR][1000 genomes]
rs2680655	1.00[AMR][1000 genomes]
rs2680667	1.00[AMR][1000 genomes]
rs6780679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs746487	1.00[AMR][1000 genomes]
rs7630968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9857905	1.00[AMR][1000 genomes]
rs9875748	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links