Variant report

Variant	rs1536820
Chromosome Location	chr9:79307633-79307634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr9:79307617-79307953	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr9:79307626-79307916	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79307128..79309630-chr9:79312231..79313981,2	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10512061	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10735649	0.80[JPT][hapmap]
rs11145009	0.82[ASN][1000 genomes]
rs2277155	0.82[MEX][hapmap]
rs3739524	0.82[MEX][hapmap]
rs488165	0.90[JPT][hapmap]
rs498266	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs506965	0.90[JPT][hapmap]
rs511545	0.90[JPT][hapmap]
rs519983	0.90[JPT][hapmap]
rs520365	0.80[JPT][hapmap]
rs530978	0.90[JPT][hapmap]
rs551262	0.90[JPT][hapmap]
rs557352	0.85[JPT][hapmap]
rs571960	0.90[JPT][hapmap]
rs579025	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs620985	0.90[JPT][hapmap]
rs625426	0.80[ASN][1000 genomes]
rs630423	0.90[JPT][hapmap]
rs677061	0.80[JPT][hapmap]
rs684639	0.94[JPT][hapmap]
rs685011	0.90[JPT][hapmap]
rs700757	0.85[CHB][hapmap];0.90[JPT][hapmap]

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	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1536820	VPS13A	cis	parietal	SCAN
rs1536820	MAP2K4	trans	parietal	SCAN
rs1536820	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79304200-79307800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:79306000-79307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:79306000-79307800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr9:79306000-79307800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr9:79306600-79307800	Flanking Active TSS	Brain Anterior Caudate	brain
7	chr9:79306600-79307800	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr9:79306600-79307800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr9:79306600-79308000	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr9:79306600-79308000	Enhancers	Gastric	stomach
11	chr9:79306800-79307800	Enhancers	Pancreas	Pancrea
12	chr9:79306800-79308000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr9:79307000-79307800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr9:79307000-79307800	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:79307200-79307800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr9:79307200-79307800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:79307200-79307800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:79307200-79307800	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr9:79307200-79307800	Enhancers	Fetal Lung	lung
20	chr9:79307200-79307800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr9:79307200-79307800	Enhancers	HSMM	muscle
22	chr9:79307200-79308000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:79307200-79308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:79307200-79308600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:79307200-79308800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:79307400-79307800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:79307400-79307800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr9:79307400-79307800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr9:79307400-79307800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr9:79307400-79307800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr9:79307400-79307800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:79307400-79307800	Enhancers	HUVEC	blood vessel
33	chr9:79307400-79307800	Active TSS	NHDF-Ad	bronchial
34	chr9:79307400-79308000	Enhancers	Fetal Intestine Small	intestine
35	chr9:79307400-79308000	Enhancers	Fetal Muscle Leg	muscle
36	chr9:79307400-79308600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr9:79307400-79308600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr9:79307400-79309000	Enhancers	Fetal Thymus	thymus
39	chr9:79307400-79310400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:79307400-79315800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:79307400-79317600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:79307600-79307800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:79307600-79307800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr9:79307600-79307800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr9:79307600-79307800	Enhancers	Fetal Brain Female	brain
46	chr9:79307600-79307800	Enhancers	Osteobl	bone
47	chr9:79307600-79308000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:79307600-79308000	Enhancers	Aorta	Aorta
49	chr9:79307600-79308000	Enhancers	Brain Substantia Nigra	brain
50	chr9:79307600-79308000	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links