Variant report

Variant	rs786320
Chromosome Location	chr9:79236165-79236166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79234093..79236437-chr9:79239287..79241420,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4745567	0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs700805	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs707742	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs786319	0.80[ASW][hapmap];0.94[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs786320	VPS13A	cis	parietal	SCAN
rs786320	KCNK17	trans	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79224600-79239000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:79224600-79244400	Weak transcription	Brain Angular Gyrus	brain
3	chr9:79224800-79239600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:79225200-79239000	Weak transcription	Brain Anterior Caudate	brain
5	chr9:79225200-79239600	Weak transcription	Brain Substantia Nigra	brain
6	chr9:79225400-79239200	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:79225400-79244000	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:79225400-79265600	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:79230200-79248200	Weak transcription	Fetal Stomach	stomach
10	chr9:79230400-79236600	Enhancers	Fetal Intestine Small	intestine
11	chr9:79230400-79241200	Enhancers	Fetal Intestine Large	intestine
12	chr9:79230600-79236600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:79230600-79241400	Weak transcription	Primary B cells from cord blood	blood
14	chr9:79230800-79236600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:79232200-79236200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr9:79232200-79236400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:79232400-79236400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:79232800-79261400	Weak transcription	Colonic Mucosa	Colon
19	chr9:79233000-79240000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:79233400-79236200	Enhancers	Adipose Nuclei	Adipose
21	chr9:79233800-79239000	Weak transcription	Gastric	stomach
22	chr9:79234000-79246000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:79234200-79236400	Enhancers	Fetal Lung	lung
24	chr9:79234200-79246000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:79234200-79252200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:79234400-79238800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:79234400-79239000	Weak transcription	Aorta	Aorta
28	chr9:79234400-79257800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:79234400-79259600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:79234600-79236600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:79234600-79238600	Weak transcription	HSMM	muscle
32	chr9:79234600-79249200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:79235200-79236400	Enhancers	Fetal Brain Female	brain
34	chr9:79235200-79236400	Enhancers	Fetal Heart	heart
35	chr9:79235200-79240600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:79235400-79236200	Enhancers	Left Ventricle	heart
37	chr9:79235400-79236200	Enhancers	Small Intestine	intestine
38	chr9:79235400-79236400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr9:79235400-79236400	Enhancers	Fetal Brain Male	brain
40	chr9:79235400-79236600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:79235400-79236600	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr9:79235600-79236200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:79235600-79236400	Enhancers	Stomach Mucosa	stomach
44	chr9:79235600-79236400	Enhancers	GM12878-XiMat	blood
45	chr9:79235600-79236800	Enhancers	Primary B cells from peripheral blood	blood
46	chr9:79235600-79236800	Enhancers	Primary hematopoietic stem cells	blood
47	chr9:79235800-79236200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:79236000-79236200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:79236000-79236200	Enhancers	Right Atrium	heart
50	chr9:79236000-79236200	Enhancers	Sigmoid Colon	Sigmoid Colon

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