Variant report

Variant	rs6476405
Chromosome Location	chr9:3331038-3331039
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12683752	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16916086	0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16916097	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs16916457	1.00[YRI][hapmap]
rs16917215	0.82[YRI][hapmap]
rs7870506	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:3306800-3337400	Weak transcription	Left Ventricle	heart
8	chr9:3308600-3337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:3310200-3337000	Weak transcription	Primary B cells from cord blood	blood
11	chr9:3311600-3338800	Weak transcription	Thymus	Thymus
12	chr9:3313200-3337000	Weak transcription	Aorta	Aorta
13	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
14	chr9:3318800-3337400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:3319000-3347800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:3319600-3337200	Weak transcription	Brain Anterior Caudate	brain
17	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:3320600-3338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:3320600-3347200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr9:3322600-3348800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:3323400-3334000	Weak transcription	Fetal Intestine Small	intestine
22	chr9:3323800-3342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:3324000-3332600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:3324000-3337200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:3324800-3337400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:3325000-3332800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:3327000-3332400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:3327400-3331400	Weak transcription	Fetal Brain Male	brain
29	chr9:3327800-3337000	Weak transcription	Ovary	ovary
30	chr9:3328200-3332000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr9:3328400-3344400	Weak transcription	Fetal Lung	lung
32	chr9:3328600-3337400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:3328800-3331800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:3328800-3332800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:3329000-3331200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr9:3329000-3334400	Enhancers	HUVEC	blood vessel
37	chr9:3329400-3332600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:3329600-3332600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:3330600-3331400	Enhancers	Osteobl	bone
41	chr9:3330600-3332000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:3330800-3331400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:3330800-3332400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:3330800-3333200	Enhancers	Fetal Heart	heart
45	chr9:3330800-3337400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:3331000-3331200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:3331000-3331200	Enhancers	NHDF-Ad	bronchial
48	chr9:3331000-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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