Variant report

Variant	rs12338885
Chromosome Location	chr9:96960952-96960953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96937218..96938797-chr9:96959660..96961275,2	K562	blood:
2	chr9:96942774..96945747-chr9:96959750..96962534,2	K562	blood:
3	chr9:96831171..96832871-chr9:96960343..96963086,2	MCF-7	breast:
4	chr9:96960924..96963618-chr9:96965476..96967579,2	K562	blood:

Variant related genes	Relation type
ENSG00000269929	Chromatin interaction
ENSG00000230262	Chromatin interaction
ENSG00000199072	Chromatin interaction
ENSG00000199165	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10512231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993068	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10993069	0.81[ASN][1000 genomes]
rs10993090	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993094	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788788	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12336926	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12337981	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12338333	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339587	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12341175	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12345069	0.88[ASN][1000 genomes]
rs12347752	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13295163	0.81[ASN][1000 genomes]
rs13439971	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13440059	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]
rs1421135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34582118	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36044301	0.81[ASN][1000 genomes]
rs55653563	0.86[ASN][1000 genomes]
rs55881323	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56006511	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62575976	0.81[ASN][1000 genomes]
rs62575977	0.81[ASN][1000 genomes]
rs62578777	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62578780	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62578801	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578804	0.86[ASN][1000 genomes]
rs7037996	0.81[ASN][1000 genomes]
rs7041934	0.81[ASN][1000 genomes]
rs7864156	0.81[ASN][1000 genomes]
rs7868381	0.81[ASN][1000 genomes]
rs7871468	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7872931	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs7873928	0.81[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	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:96942400-96964000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:96946200-96962800	Weak transcription	Gastric	stomach
4	chr9:96946200-96965000	Weak transcription	NHLF	lung
5	chr9:96946800-96965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:96947000-96966200	Weak transcription	Fetal Kidney	kidney
7	chr9:96955000-96964600	Weak transcription	Ovary	ovary
8	chr9:96955400-96962200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:96955800-96962800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:96956800-96963000	Strong transcription	HSMM	muscle
11	chr9:96956800-96963400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:96957000-96963000	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr9:96957400-96961200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr9:96957800-96961600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:96958400-96962600	Weak transcription	Primary T cells from cord blood	blood
16	chr9:96958400-96963000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:96958400-96963800	Weak transcription	Primary B cells from cord blood	blood
18	chr9:96958600-96963400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:96959000-96961400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:96959200-96961200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:96959200-96961200	Strong transcription	NHEK	skin
22	chr9:96959200-96961400	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr9:96959400-96961000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:96959400-96961000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:96959400-96961200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:96959400-96961200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr9:96959400-96961400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:96959400-96961800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:96959400-96963600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:96959600-96964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:96959800-96961000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:96959800-96961000	Weak transcription	Lung	lung
33	chr9:96959800-96962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:96959800-96963400	Weak transcription	Fetal Brain Male	brain
35	chr9:96960000-96964000	Weak transcription	Left Ventricle	heart
36	chr9:96960200-96961400	Enhancers	Esophagus	oesophagus
37	chr9:96960200-96961800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:96960200-96962400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:96960200-96965000	Weak transcription	Adipose Nuclei	Adipose
40	chr9:96960400-96961200	Weak transcription	Psoas Muscle	Psoas
41	chr9:96960400-96962800	Weak transcription	Osteobl	bone
42	chr9:96960400-96964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:96960400-96966000	Weak transcription	HSMMtube	muscle
44	chr9:96960600-96962600	Weak transcription	Aorta	Aorta
45	chr9:96960800-96961000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:96960800-96961000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr9:96960800-96961200	Weak transcription	Fetal Lung	lung
48	chr9:96960800-96961200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr9:96960800-96961400	Enhancers	Right Ventricle	heart

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