Variant report

Variant	rs2073886
Chromosome Location	chr9:136804211-136804212
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	chr9:136802379..136804423-chr9:136852709..136855178,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2073829	0.82[JPT][hapmap]
rs2519102	1.00[CEU][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes]
rs2519103	0.82[JPT][hapmap]
rs2519104	0.83[JPT][hapmap]
rs2519802	0.83[JPT][hapmap]
rs2519803	0.83[JPT][hapmap]
rs2519805	0.94[CEU][hapmap];0.80[JPT][hapmap];0.98[EUR][1000 genomes]
rs2810530	0.83[CEU][hapmap];0.98[EUR][1000 genomes]
rs2810531	0.86[JPT][hapmap]
rs2810532	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894127	chr9:136747832-136811772	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv615741	chr9:136785840-136807283	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2073886	GTF3C5	cis	cerebellum	SCAN
rs2073886	ABL1	cis	parietal	SCAN
rs2073886	BRD3	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136753000-136813200	Weak transcription	Aorta	Aorta
2	chr9:136781200-136804600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:136782000-136809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:136794000-136807400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:136795600-136808600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:136796800-136805600	Weak transcription	Fetal Heart	heart
8	chr9:136797400-136804600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr9:136797800-136811000	Weak transcription	A549	lung
10	chr9:136799400-136805800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:136800800-136804600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:136801200-136805400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:136801200-136805400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:136801200-136807400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:136801200-136807400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:136801200-136807400	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:136801200-136808200	Weak transcription	Esophagus	oesophagus
19	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
20	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
22	chr9:136801400-136809200	Weak transcription	HUVEC	blood vessel
23	chr9:136801400-136809800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:136801400-136810200	Weak transcription	Placenta	Placenta
25	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:136801800-136805200	Strong transcription	Fetal Stomach	stomach
27	chr9:136802000-136804400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:136802000-136804400	Strong transcription	HMEC	breast
29	chr9:136802000-136804400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr9:136802000-136805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:136802000-136805200	Strong transcription	HepG2	liver
32	chr9:136802000-136807800	Weak transcription	Small Intestine	intestine
33	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
34	chr9:136802200-136804400	Strong transcription	Liver	Liver
35	chr9:136802200-136804400	Strong transcription	GM12878-XiMat	blood
36	chr9:136802200-136804800	Strong transcription	Fetal Intestine Large	intestine
37	chr9:136802200-136805800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
39	chr9:136802400-136804400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:136802400-136804400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr9:136802400-136805200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:136802600-136804400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:136802600-136804400	Strong transcription	Osteobl	bone
44	chr9:136802600-136810200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:136802800-136804400	Strong transcription	Brain Germinal Matrix	brain
46	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
47	chr9:136803000-136804400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:136803000-136804600	Weak transcription	Fetal Brain Male	brain
49	chr9:136803000-136807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:136803000-136813000	Weak transcription	Fetal Lung	lung

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