Variant report

Variant	rs12339886
Chromosome Location	chr9:5966355-5966356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	1.00[EUR][1000 genomes]
rs10125832	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975350	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10975351	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975367	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10975372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975377	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12337300	1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12337445	1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12337790	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs12339713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339889	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340153	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12340531	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341021	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342166	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12342282	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12343325	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12345849	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351533	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12352918	0.90[AFR][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.84[MKK][hapmap]
rs28431078	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	1.00[EUR][1000 genomes]
rs58291302	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60037728	1.00[EUR][1000 genomes]
rs7022080	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7029847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385128	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389044	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73397376	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73399307	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73639554	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73639568	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7854980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7858084	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858846	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7874032	0.92[ASN][1000 genomes]
rs7875607	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299025	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv613204	chr9:5931216-5971977	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5923000-5969000	Weak transcription	Fetal Stomach	stomach
2	chr9:5923200-5968200	Weak transcription	Fetal Muscle Leg	muscle
3	chr9:5923200-5971800	Weak transcription	NHEK	skin
4	chr9:5923200-5972400	Weak transcription	Aorta	Aorta
5	chr9:5924600-5967400	Weak transcription	Brain Anterior Caudate	brain
6	chr9:5924600-5968600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:5924600-5977000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:5924600-5977000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:5924800-5967600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr9:5925200-5968400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:5926800-5972600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:5933600-5968400	Weak transcription	Fetal Intestine Large	intestine
13	chr9:5934000-5967200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:5934000-5967600	Weak transcription	Placenta	Placenta
15	chr9:5934000-5968400	Weak transcription	Left Ventricle	heart
16	chr9:5934200-5967600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:5940000-6006800	Weak transcription	Gastric	stomach
18	chr9:5940200-5973800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
20	chr9:5948200-5976800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:5948400-5968400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:5948400-5968800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:5949000-5968000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:5949400-5967200	Weak transcription	Fetal Thymus	thymus
25	chr9:5949400-5968600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:5949600-5967400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr9:5949600-5967400	Weak transcription	Adipose Nuclei	Adipose
28	chr9:5949600-5968600	Weak transcription	HSMM	muscle
29	chr9:5949600-5968800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:5949600-5969000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:5949600-5976400	Weak transcription	Fetal Heart	heart
32	chr9:5949800-5967200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:5949800-5967200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:5949800-5967200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:5949800-5967600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:5949800-5976800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:5950200-5968600	Weak transcription	Dnd41	blood
38	chr9:5950200-5973600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:5950400-5967600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:5950400-5968600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:5950600-5967600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:5950800-5967200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:5951200-5976800	Weak transcription	Psoas Muscle	Psoas
45	chr9:5952400-5971400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr9:5952400-5973600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:5952400-5973600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:5952400-5973600	Weak transcription	Ovary	ovary
49	chr9:5952400-5976600	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:5952600-5967800	Weak transcription	NHDF-Ad	bronchial

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