Variant report

Variant	rs11145009
Chromosome Location	chr9:79307454-79307455
allele	A/G
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	ZNF263	chr9:79306837-79307571	HEK293-T-REx	kidney:	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: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10512061	0.82[ASN][1000 genomes]
rs1536820	0.82[ASN][1000 genomes]
rs2487263	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2553212	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2553213	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs488165	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs489069	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs498266	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511545	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519983	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs520365	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs537903	0.80[AFR][1000 genomes]
rs551262	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs579025	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625426	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641088	0.80[AFR][1000 genomes]
rs677061	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684639	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs685011	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs700757	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs786597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11145009	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:65 , 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	chr9:79305000-79307600	Weak transcription	Aorta	Aorta
4	chr9:79305200-79307600	Enhancers	Stomach Mucosa	stomach
5	chr9:79306000-79307600	Active TSS	Fetal Brain Female	brain
6	chr9:79306000-79307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:79306000-79307800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:79306000-79307800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr9:79306600-79307600	Flanking Active TSS	Osteobl	bone
10	chr9:79306600-79307800	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr9:79306600-79307800	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr9:79306600-79307800	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr9:79306600-79308000	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr9:79306600-79308000	Enhancers	Gastric	stomach
15	chr9:79306800-79307600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:79306800-79307600	Active TSS	Brain Germinal Matrix	brain
17	chr9:79306800-79307600	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr9:79306800-79307800	Enhancers	Pancreas	Pancrea
19	chr9:79306800-79308000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr9:79307000-79307800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr9:79307000-79307800	Enhancers	Primary hematopoietic stem cells	blood
22	chr9:79307200-79307600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:79307200-79307600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr9:79307200-79307600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:79307200-79307600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr9:79307200-79307600	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr9:79307200-79307600	Enhancers	Fetal Intestine Large	intestine
28	chr9:79307200-79307600	Enhancers	Fetal Kidney	kidney
29	chr9:79307200-79307600	Enhancers	HSMMtube	muscle
30	chr9:79307200-79307800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr9:79307200-79307800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:79307200-79307800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:79307200-79307800	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr9:79307200-79307800	Enhancers	Fetal Lung	lung
35	chr9:79307200-79307800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr9:79307200-79307800	Enhancers	HSMM	muscle
37	chr9:79307200-79308000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:79307200-79308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:79307200-79308600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:79307200-79308800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:79307400-79307600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr9:79307400-79307600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr9:79307400-79307600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:79307400-79307600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:79307400-79307600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:79307400-79307600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr9:79307400-79307600	Flanking Active TSS	Fetal Brain Male	brain
48	chr9:79307400-79307600	Active TSS	Fetal Muscle Trunk	muscle
49	chr9:79307400-79307600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:79307400-79307800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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