Variant report

Variant	rs73820009
Chromosome Location	chr3:24634282-24634283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24315110..24317953-chr3:24633288..24636026,3	MCF-7	breast:
2	chr3:24567024..24569936-chr3:24632741..24634847,2	K562	blood:
3	chr3:24633657..24635628-chr3:24639189..24641484,2	MCF-7	breast:
4	chr3:24535097..24538455-chr3:24631744..24636761,7	MCF-7	breast:
5	chr3:24350162..24351776-chr3:24632242..24634979,2	MCF-7	breast:
6	chr3:24599960..24602220-chr3:24631656..24634494,2	K562	blood:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10212177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561078	0.94[ASN][1000 genomes]
rs1865714	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2196429	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73820005	0.94[ASN][1000 genomes]
rs7632924	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7649819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650964	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7653148	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830855	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9836150	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9856426	0.94[EUR][1000 genomes];0.94[ASN][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	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24630800-24640800	Weak transcription	Small Intestine	intestine
2	chr3:24631200-24636000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:24631400-24634600	Enhancers	HMEC	breast
4	chr3:24631400-24635200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:24631600-24634400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:24631600-24634400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:24631800-24634600	Enhancers	Fetal Intestine Large	intestine
8	chr3:24632000-24636200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:24632000-24637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:24632000-24640000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:24632200-24635800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:24632200-24637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:24632600-24634600	Enhancers	Fetal Intestine Small	intestine
14	chr3:24632800-24634600	Enhancers	Primary hematopoietic stem cells	blood
15	chr3:24633000-24634400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:24633000-24634600	Enhancers	Hela-S3	cervix
17	chr3:24633200-24640000	Weak transcription	Fetal Lung	lung
18	chr3:24633600-24637000	Weak transcription	Stomach Mucosa	stomach
19	chr3:24633600-24640000	Weak transcription	NHDF-Ad	bronchial
20	chr3:24633800-24634600	Enhancers	NHEK	skin
21	chr3:24633800-24636000	Weak transcription	Fetal Brain Male	brain
22	chr3:24633800-24637200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:24633800-24639600	Weak transcription	HUVEC	blood vessel
24	chr3:24633800-24640200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:24634000-24634600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:24634000-24635200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:24634200-24635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:24634200-24635600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:24634200-24640000	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links