Variant report

Variant	rs13440059
Chromosome Location	chr9:96933066-96933067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96771017..96773474-chr9:96932074..96933586,2	MCF-7	breast:
2	chr9:96913449..96915470-chr9:96932041..96933932,2	MCF-7	breast:
3	chr9:96829354..96831525-chr9:96932462..96934545,2	K562	blood:
4	chr9:96931258..96933517-chr9:97020161..97023083,3	K562	blood:
5	chr9:96827846..96829961-chr9:96932041..96934679,2	MCF-7	breast:
6	chr9:96845064..96846581-chr9:96932043..96934956,2	K562	blood:

Variant related genes	Relation type
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10512231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993068	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10993069	0.90[ASN][1000 genomes]
rs10993090	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11788788	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12336926	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12337981	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12338333	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12338885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12341175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12345069	0.83[AFR][1000 genomes]
rs12347752	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13295163	0.90[ASN][1000 genomes]
rs13439971	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1421135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34582118	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34765284	0.86[ASN][1000 genomes]
rs36044301	0.90[ASN][1000 genomes]
rs55881323	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56006511	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62575976	0.90[ASN][1000 genomes]
rs62575977	0.90[ASN][1000 genomes]
rs62578777	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62578780	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62578801	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7037996	0.90[ASN][1000 genomes]
rs7041934	0.90[ASN][1000 genomes]
rs7864156	0.90[ASN][1000 genomes]
rs7868381	0.90[ASN][1000 genomes]
rs7871468	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7872931	1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.86[MKK][hapmap];0.83[AFR][1000 genomes]
rs7873928	0.90[ASN][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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3435412	chr9:96924949-96935312	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96927800-96933200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:96929600-96933400	Weak transcription	Spleen	Spleen
3	chr9:96929600-96936400	Weak transcription	Gastric	stomach
4	chr9:96929600-96938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:96929800-96933400	Weak transcription	Lung	lung
6	chr9:96929800-96933400	Weak transcription	Pancreas	Pancrea
7	chr9:96929800-96936000	Weak transcription	Esophagus	oesophagus
8	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:96930000-96933600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:96930000-96936200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:96930200-96933800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:96930400-96933400	Weak transcription	Small Intestine	intestine
14	chr9:96930400-96935400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr9:96930400-96938200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr9:96930600-96933800	Enhancers	Primary T cells from cord blood	blood
17	chr9:96930600-96934800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:96930600-96935400	Weak transcription	Fetal Thymus	thymus
19	chr9:96930600-96935600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr9:96930600-96935800	Weak transcription	Placenta	Placenta
21	chr9:96930600-96937600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:96930600-96943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:96930600-96943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:96930800-96933400	Weak transcription	Colonic Mucosa	Colon
25	chr9:96930800-96933600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:96931000-96933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:96931000-96934600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr9:96931000-96935400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr9:96931000-96935400	Enhancers	Colon Smooth Muscle	Colon
30	chr9:96931000-96936000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr9:96931000-96937200	Enhancers	Fetal Heart	heart
32	chr9:96931200-96933400	Enhancers	Fetal Lung	lung
33	chr9:96931200-96933800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:96931200-96934400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:96931200-96934600	Enhancers	Brain Hippocampus Middle	brain
36	chr9:96931200-96935400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:96931200-96935400	Enhancers	Stomach Smooth Muscle	stomach
38	chr9:96931200-96935600	Enhancers	Liver	Liver
39	chr9:96931200-96935600	Weak transcription	Stomach Mucosa	stomach
40	chr9:96931200-96936000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:96931200-96936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr9:96931200-96936400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:96931200-96938200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr9:96931200-96938800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr9:96931400-96935800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:96931600-96933400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr9:96931800-96933400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:96931800-96933400	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:96931800-96933400	Weak transcription	Left Ventricle	heart

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