Variant report

Variant	rs9879944
Chromosome Location	chr3:79020897-79020898
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:79019214..79022375-chr3:79066992..79070586,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514741	0.82[AMR][1000 genomes]
rs13321050	0.86[AFR][1000 genomes]
rs13321792	0.85[AFR][1000 genomes]
rs13321973	0.86[AFR][1000 genomes]
rs13325521	0.86[AFR][1000 genomes]
rs17016641	0.86[AFR][1000 genomes]
rs17016648	0.81[AFR][1000 genomes]
rs17016656	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs28412538	0.93[AFR][1000 genomes]
rs28667917	0.88[AFR][1000 genomes]
rs57432814	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58608513	0.81[AFR][1000 genomes]
rs72906176	0.86[AFR][1000 genomes]
rs72910206	0.89[AFR][1000 genomes]
rs72910208	0.89[AFR][1000 genomes]
rs72910211	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72910220	0.82[AMR][1000 genomes]
rs72910224	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9809330	0.86[AFR][1000 genomes]
rs9818387	0.88[AFR][1000 genomes]
rs9833345	0.82[AMR][1000 genomes]
rs9838831	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9853126	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9858080	0.86[AFR][1000 genomes]
rs9870336	0.83[AFR][1000 genomes];0.82[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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr3:79001000-79024200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:79006800-79023600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:79007000-79023400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:79011400-79027400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:79013400-79021800	Weak transcription	Psoas Muscle	Psoas
6	chr3:79015400-79022200	Weak transcription	Ovary	ovary
7	chr3:79016400-79022000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:79016800-79023600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:79016800-79024800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:79018000-79027600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:79018200-79027600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:79018600-79024400	Weak transcription	Fetal Lung	lung
13	chr3:79018600-79027600	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:79018600-79027600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:79018800-79021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:79018800-79022200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:79018800-79023000	Weak transcription	NHDF-Ad	bronchial
18	chr3:79019000-79021200	Weak transcription	HMEC	breast
19	chr3:79019000-79022200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:79019000-79022800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:79019000-79023600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:79019200-79023000	Weak transcription	HSMM	muscle
23	chr3:79019200-79025400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:79019600-79025400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:79019600-79027400	Weak transcription	Brain Anterior Caudate	brain
26	chr3:79020200-79021800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:79020200-79022000	Weak transcription	Osteobl	bone
28	chr3:79020200-79022400	Enhancers	HepG2	liver
29	chr3:79020600-79027800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links