Variant report

Variant	rs2026143
Chromosome Location	chr9:116718877-116718878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116718450..116721380-chr9:116821221..116823441,2	MCF-7	breast:
2	chr9:116714751..116717397-chr9:116717561..116719359,3	MCF-7	breast:
3	chr9:116717988..116720152-chr9:116724018..116725544,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10119978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10448275	0.96[CEU][hapmap]
rs10448276	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739396	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10759664	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759665	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817536	0.82[EUR][1000 genomes]
rs10817537	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10817539	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10817541	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10982008	0.83[EUR][1000 genomes]
rs10982009	0.89[ASN][1000 genomes]
rs10982015	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982017	0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12551141	0.95[CHB][hapmap]
rs1330166	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1536962	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1536965	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544102	0.85[CEU][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1888161	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2418260	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2418261	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2761688	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2773396	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2900570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900571	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4979298	0.95[CHB][hapmap]
rs4979307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7032101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7046776	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7867998	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7869027	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs814680	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs814686	0.88[ASN][1000 genomes]
rs814696	0.82[CEU][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs871806	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs871808	0.96[CEU][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116692000-116719400	Weak transcription	HMEC	breast
2	chr9:116696200-116719800	Weak transcription	Gastric	stomach
3	chr9:116703600-116719800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:116708800-116726400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:116709000-116720600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:116710400-116719600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:116710800-116723000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:116712000-116719800	Weak transcription	Fetal Intestine Small	intestine
9	chr9:116712800-116726400	Weak transcription	Brain Germinal Matrix	brain
10	chr9:116713000-116719400	Weak transcription	Stomach Mucosa	stomach
11	chr9:116713200-116719800	Weak transcription	Spleen	Spleen
12	chr9:116713400-116719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116714400-116721200	Enhancers	NHDF-Ad	bronchial
14	chr9:116714600-116719200	Enhancers	NH-A	brain
15	chr9:116714600-116719600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:116714600-116720400	Enhancers	Osteobl	bone
17	chr9:116714600-116721600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:116714600-116722400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:116715000-116721000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:116715000-116721200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:116716000-116720800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:116716200-116730000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:116716400-116719800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:116716600-116719000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:116716600-116720600	Enhancers	Fetal Kidney	kidney
26	chr9:116716800-116721000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:116716800-116723000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:116717000-116720800	Enhancers	Adipose Nuclei	Adipose
29	chr9:116717000-116720800	Enhancers	Fetal Lung	lung
30	chr9:116717000-116721200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:116717000-116723400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:116717000-116730000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:116717000-116733200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:116717200-116719600	Enhancers	A549	lung
35	chr9:116717200-116720400	Weak transcription	Left Ventricle	heart
36	chr9:116717200-116720400	Weak transcription	Right Atrium	heart
37	chr9:116717200-116754600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:116717400-116719600	Weak transcription	Right Ventricle	heart
39	chr9:116717400-116735600	Weak transcription	Fetal Heart	heart
40	chr9:116717600-116719600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:116717600-116719800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:116717600-116719800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:116717600-116730200	Weak transcription	Psoas Muscle	Psoas
44	chr9:116717800-116719600	Weak transcription	Liver	Liver
45	chr9:116717800-116719600	Weak transcription	Brain Anterior Caudate	brain
46	chr9:116717800-116720800	Enhancers	HSMMtube	muscle
47	chr9:116717800-116724800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:116718000-116719200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:116718000-116731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:116718200-116719200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links