Variant report

Variant	rs820562
Chromosome Location	chr3:112464213-112464214
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	chr3:112461762..112464702-chr3:112469113..112471587,3	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs820557	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820558	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112458400-112465600	Weak transcription	NHLF	lung
2	chr3:112458400-112467800	Weak transcription	Stomach Mucosa	stomach
3	chr3:112458800-112467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:112459000-112467000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:112459000-112470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:112459200-112466400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:112459200-112467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:112460200-112464800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:112460800-112465600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:112461400-112466400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:112461400-112466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:112461800-112465800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:112462600-112464800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:112462600-112468000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:112462800-112464600	Enhancers	Fetal Lung	lung
16	chr3:112462800-112464600	Enhancers	Fetal Stomach	stomach
17	chr3:112463000-112465800	Enhancers	Fetal Thymus	thymus
18	chr3:112463000-112465800	Enhancers	NHDF-Ad	bronchial
19	chr3:112463400-112465000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:112463600-112464400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:112463600-112464400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:112463800-112464600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:112463800-112465000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:112463800-112465800	Enhancers	Thymus	Thymus
25	chr3:112463800-112466000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:112464000-112464400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:112464000-112465000	Enhancers	GM12878-XiMat	blood
28	chr3:112464000-112465200	Weak transcription	Osteobl	bone
29	chr3:112464000-112465400	Enhancers	A549	lung
30	chr3:112464200-112464600	Weak transcription	K562	blood
31	chr3:112464200-112468000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:112464200-112469200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links