Variant report

Variant	rs12001895
Chromosome Location	chr9:3287574-3287575
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1013026	0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11999151	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs12000700	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12001962	1.00[EUR][1000 genomes]
rs12002029	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs12002102	1.00[EUR][1000 genomes]
rs12002158	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs12002701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003162	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003329	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs12004859	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12006321	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12335756	1.00[EUR][1000 genomes]
rs16916437	0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16917139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16917267	1.00[EUR][1000 genomes]
rs2229356	1.00[EUR][1000 genomes]
rs2991288	1.00[EUR][1000 genomes]
rs56663916	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59102176	0.89[AFR][1000 genomes];1.00[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	1.00[EUR][1000 genomes]
rs7022295	0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024463	1.00[EUR][1000 genomes]
rs7025835	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7028013	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7032669	0.92[AFR][1000 genomes]
rs7033352	1.00[EUR][1000 genomes]
rs7034430	1.00[EUR][1000 genomes]
rs7035860	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs7851137	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7854551	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858027	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872539	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1032529	chr9:3254763-3319778	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv539941	chr9:3254763-3319778	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
3	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:3242200-3287800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:3251600-3292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:3255000-3293000	Weak transcription	Small Intestine	intestine
8	chr9:3255800-3292800	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:3256800-3293400	Weak transcription	Right Ventricle	heart
10	chr9:3257000-3289000	Weak transcription	Fetal Brain Male	brain
11	chr9:3257200-3290200	Weak transcription	Brain Germinal Matrix	brain
12	chr9:3257200-3290200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:3257200-3290200	Weak transcription	Brain Substantia Nigra	brain
14	chr9:3257200-3294000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:3257200-3294400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:3257400-3289000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:3263200-3294200	Weak transcription	Fetal Lung	lung
18	chr9:3263200-3294600	Weak transcription	Esophagus	oesophagus
19	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:3265200-3291000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:3265400-3293000	Weak transcription	Brain Angular Gyrus	brain
22	chr9:3265600-3292600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:3268600-3292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:3270400-3287600	Weak transcription	Adipose Nuclei	Adipose
26	chr9:3270800-3292600	Weak transcription	Brain Anterior Caudate	brain
27	chr9:3271000-3289200	Weak transcription	Thymus	Thymus
28	chr9:3271000-3289600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:3272000-3291000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:3272000-3292800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:3272000-3302800	Weak transcription	Ovary	ovary
32	chr9:3272600-3288600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:3274600-3287800	Weak transcription	Fetal Intestine Large	intestine
34	chr9:3275600-3288800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:3275800-3294600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:3275800-3295600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:3276600-3295000	Weak transcription	Fetal Thymus	thymus
38	chr9:3276800-3291000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:3276800-3299400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr9:3277400-3310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:3278800-3289200	Weak transcription	Dnd41	blood
43	chr9:3280600-3288400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:3282000-3287600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:3285400-3288200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr9:3285400-3288400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr9:3285800-3287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:3285800-3288400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:3285800-3288800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr9:3286000-3288200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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