Variant report

Variant	rs9886680
Chromosome Location	chr9:79132141-79132142
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79072653..79077214-chr9:79131036..79138388,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT1-1	chr9:79131410-79133074	NONHSAT131953

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11144942	0.81[JPT][hapmap]
rs539188	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56097164	0.81[ASN][1000 genomes]
rs585575	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs621293	0.90[CHB][hapmap]
rs9886712	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv437089	chr9:79116975-79139590	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 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	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
2	chr9:79118600-79134200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:79118800-79136400	Weak transcription	Gastric	stomach
4	chr9:79118800-79145800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr9:79119200-79134000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:79119800-79132200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:79120400-79134000	Weak transcription	Fetal Intestine Large	intestine
8	chr9:79120400-79145200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:79126400-79140800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:79128000-79133400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:79128000-79133400	Weak transcription	HMEC	breast
12	chr9:79128200-79134000	Weak transcription	HSMMtube	muscle
13	chr9:79128400-79141000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:79128600-79135800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:79129200-79152000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:79130400-79132800	Strong transcription	Primary B cells from cord blood	blood
17	chr9:79131000-79132200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:79131000-79132800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:79131000-79136800	Strong transcription	Osteobl	bone
20	chr9:79131200-79132400	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:79131200-79132800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:79131200-79132800	Enhancers	GM12878-XiMat	blood
23	chr9:79131400-79132600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:79131600-79132200	Strong transcription	NHDF-Ad	bronchial
25	chr9:79131600-79134000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:79131600-79141000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:79131800-79132400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr9:79131800-79132800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:79132000-79132200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:79132000-79132600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr9:79132000-79132800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:79132000-79132800	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links