Variant report

Variant	rs16917139
Chromosome Location	chr9:3337260-3337261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1013026	1.00[EUR][1000 genomes]
rs11999151	0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12000700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001895	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001962	1.00[EUR][1000 genomes]
rs12002029	0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12002102	1.00[EUR][1000 genomes]
rs12002158	0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12002701	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003162	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003329	0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12004859	0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12006321	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12335756	1.00[EUR][1000 genomes]
rs16916437	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16917267	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2229356	1.00[EUR][1000 genomes]
rs2991288	1.00[EUR][1000 genomes]
rs56663916	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59102176	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs646522	1.00[EUR][1000 genomes]
rs660374	1.00[EUR][1000 genomes]
rs688017	1.00[EUR][1000 genomes]
rs7020882	0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7022295	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024463	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs7025835	1.00[EUR][1000 genomes]
rs7028013	0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7033352	1.00[EUR][1000 genomes]
rs7034430	1.00[EUR][1000 genomes]
rs7035860	1.00[EUR][1000 genomes]
rs7851137	0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853034	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7854551	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858027	1.00[EUR][1000 genomes]
rs7863972	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs7872539	1.00[EUR][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:50 , 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	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:3306800-3337400	Weak transcription	Left Ventricle	heart
7	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:3311600-3338800	Weak transcription	Thymus	Thymus
9	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
10	chr9:3318800-3337400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:3319000-3347800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:3320600-3338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:3320600-3347200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:3322600-3348800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr9:3323800-3342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:3324800-3337400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:3328400-3344400	Weak transcription	Fetal Lung	lung
19	chr9:3328600-3337400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:3330800-3337400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:3331000-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:3331400-3337400	Weak transcription	Osteobl	bone
24	chr9:3331600-3337400	Weak transcription	NHDF-Ad	bronchial
25	chr9:3333000-3352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:3336600-3338400	Enhancers	Stomach Smooth Muscle	stomach
27	chr9:3337000-3337400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:3337000-3337600	Enhancers	Aorta	Aorta
29	chr9:3337000-3337600	Enhancers	Right Atrium	heart
30	chr9:3337000-3337600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr9:3337000-3337600	Enhancers	HUVEC	blood vessel
32	chr9:3337000-3337800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:3337000-3337800	Strong transcription	Primary B cells from cord blood	blood
34	chr9:3337000-3337800	Enhancers	Brain Angular Gyrus	brain
35	chr9:3337000-3337800	Enhancers	Brain Substantia Nigra	brain
36	chr9:3337000-3337800	Enhancers	Ovary	ovary
37	chr9:3337000-3337800	Enhancers	Psoas Muscle	Psoas
38	chr9:3337000-3338000	Enhancers	Brain Hippocampus Middle	brain
39	chr9:3337000-3338000	Enhancers	Colon Smooth Muscle	Colon
40	chr9:3337000-3338400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:3337000-3338600	Enhancers	NHLF	lung
42	chr9:3337000-3338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:3337000-3338800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:3337200-3337600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:3337200-3337800	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:3337200-3337800	Enhancers	Rectal Smooth Muscle	rectum
47	chr9:3337200-3337800	Enhancers	Small Intestine	intestine
48	chr9:3337200-3338000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr9:3337200-3338200	Enhancers	Brain Anterior Caudate	brain
50	chr9:3337200-3338800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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