Variant report

Variant	rs3012680
Chromosome Location	chr9:3278237-3278238
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10429463	0.81[ASN][1000 genomes]
rs1147822	0.81[ASN][1000 genomes]
rs11998979	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12004744	0.83[ASN][1000 genomes]
rs16916423	0.88[ASN][1000 genomes]
rs17658724	0.86[ASN][1000 genomes]
rs17658838	0.86[ASN][1000 genomes]
rs2304928	0.81[ASN][1000 genomes]
rs2920363	0.83[ASN][1000 genomes]
rs2920375	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2991297	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2991298	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2991300	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3012686	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3012688	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3012692	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs490961	0.81[ASN][1000 genomes]
rs494348	0.83[ASN][1000 genomes]
rs506149	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs576347	0.86[ASN][1000 genomes]
rs58010475	0.86[ASN][1000 genomes]
rs617047	0.86[ASN][1000 genomes]
rs619401	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs625941	0.83[ASN][1000 genomes]
rs656686	0.83[ASN][1000 genomes]
rs658123	0.91[ASN][1000 genomes]
rs72699014	0.81[ASN][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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
2	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
3	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
5	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:3242200-3287800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:3243800-3279200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:3246800-3287000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:3251600-3292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:3252800-3278600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3254200-3285600	Weak transcription	Fetal Heart	heart
13	chr9:3255000-3293000	Weak transcription	Small Intestine	intestine
14	chr9:3255800-3292800	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:3256800-3293400	Weak transcription	Right Ventricle	heart
16	chr9:3257000-3289000	Weak transcription	Fetal Brain Male	brain
17	chr9:3257200-3290200	Weak transcription	Brain Germinal Matrix	brain
18	chr9:3257200-3290200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:3257200-3290200	Weak transcription	Brain Substantia Nigra	brain
20	chr9:3257200-3294000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:3257200-3294400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:3257400-3279000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:3257400-3289000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:3257800-3285800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:3261400-3281400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr9:3263000-3286800	Weak transcription	Liver	Liver
27	chr9:3263200-3278400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:3263200-3294200	Weak transcription	Fetal Lung	lung
29	chr9:3263200-3294600	Weak transcription	Esophagus	oesophagus
30	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:3263800-3286600	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:3265200-3280200	Weak transcription	Aorta	Aorta
33	chr9:3265200-3291000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:3265400-3287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:3265400-3293000	Weak transcription	Brain Angular Gyrus	brain
36	chr9:3265600-3292600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr9:3268600-3292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:3270400-3287600	Weak transcription	Adipose Nuclei	Adipose
40	chr9:3270800-3292600	Weak transcription	Brain Anterior Caudate	brain
41	chr9:3271000-3289200	Weak transcription	Thymus	Thymus
42	chr9:3271000-3289600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:3271400-3287200	Weak transcription	Left Ventricle	heart
44	chr9:3272000-3291000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:3272000-3292800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:3272000-3302800	Weak transcription	Ovary	ovary
47	chr9:3272200-3280400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:3272600-3288600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:3272800-3287400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:3274600-3287800	Weak transcription	Fetal Intestine Large	intestine

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