Variant report

Variant	rs500952
Chromosome Location	chr9:79307176-79307177
allele	C/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	USF1	chr9:79306869-79307383	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr9:79306867-79307294	SK-N-SH	brain:	n/a	n/a
3	YY1	chr9:79306884-79307282	SK-N-SH_RA	brain:	n/a	chr9:79307092-79307104
4	USF1	chr9:79306831-79307382	SK-N-SH	brain:	n/a	n/a
5	YY1	chr9:79306873-79307238	H1-hESC	embryonic stem cell:	n/a	chr9:79307092-79307104
6	USF1	chr9:79306903-79307337	HCT-116	colon:	n/a	n/a
7	YY1	chr9:79306693-79307259	SK-N-SH	brain:	n/a	chr9:79307092-79307104 chr9:79306837-79306848
8	POLR2A	chr9:79306690-79307269	H1-neurons	neurons:	n/a	n/a
9	MAX	chr9:79307023-79307241	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr9:79306570-79307336	H1-neurons	neurons:	n/a	chr9:79306753-79306766
11	YY1	chr9:79306800-79307297	SK-N-SH_RA	brain:	n/a	chr9:79307092-79307104 chr9:79306837-79306848
12	USF1	chr9:79306812-79307407	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZNF263	chr9:79306837-79307571	HEK293-T-REx	kidney:	n/a	n/a
14	USF2	chr9:79306854-79307317	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr9:79306859-79307347	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr9:79306709-79307279	H1-hESC	embryonic stem cell:	n/a	chr9:79307092-79307104 chr9:79306837-79306848
17	TAF1	chr9:79306813-79307297	H1-neurons	neurons:	n/a	n/a
18	USF1	chr9:79306931-79307252	K562	blood:	n/a	n/a
19	TAF1	chr9:79306866-79307177	SK-N-SH	brain:	n/a	n/a
20	TAF1	chr9:79306865-79307277	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr9:79306757-79307376	HCT-116	colon:	n/a	n/a
22	POLR2A	chr9:79306671-79307283	H1-neurons	neurons:	n/a	n/a
23	USF1	chr9:79306731-79307447	SK-N-SH	brain:	n/a	n/a
24	SIN3A	chr9:79306687-79307229	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr9:79306937-79307248	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr9:79307120-79307270	HEK293	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: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10869799	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs509489	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs512110	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517634	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554143	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs556725	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561970	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566584	0.89[ASN][1000 genomes]
rs572737	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs591411	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594586	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs611461	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs615187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs618145	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620321	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs620476	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620552	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626416	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs646698	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs650682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678943	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680729	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs680775	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7033978	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7870516	1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs500952	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:99 , 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	chr9:79305200-79307200	Enhancers	Colon Smooth Muscle	Colon
5	chr9:79305200-79307600	Enhancers	Stomach Mucosa	stomach
6	chr9:79306000-79307200	Active TSS	Brain Angular Gyrus	brain
7	chr9:79306000-79307200	Enhancers	Lung	lung
8	chr9:79306000-79307600	Active TSS	Fetal Brain Female	brain
9	chr9:79306000-79307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79306000-79307800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:79306000-79307800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr9:79306400-79307200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:79306400-79307200	Enhancers	Colonic Mucosa	Colon
14	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr9:79306400-79307400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr9:79306400-79307400	Active TSS	Fetal Brain Male	brain
18	chr9:79306400-79307400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr9:79306600-79307200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:79306600-79307200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr9:79306600-79307200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:79306600-79307200	Active TSS	Right Atrium	heart
23	chr9:79306600-79307400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr9:79306600-79307400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr9:79306600-79307400	Active TSS	Primary T cells from cord blood	blood
26	chr9:79306600-79307400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:79306600-79307400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:79306600-79307400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr9:79306600-79307400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr9:79306600-79307400	Flanking Active TSS	HUVEC	blood vessel
31	chr9:79306600-79307600	Flanking Active TSS	Osteobl	bone
32	chr9:79306600-79307800	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr9:79306600-79307800	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr9:79306600-79307800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr9:79306600-79308000	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr9:79306600-79308000	Enhancers	Gastric	stomach
37	chr9:79306800-79307200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
38	chr9:79306800-79307200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:79306800-79307200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
40	chr9:79306800-79307200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:79306800-79307200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
42	chr9:79306800-79307200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:79306800-79307200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr9:79306800-79307200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:79306800-79307200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:79306800-79307200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
47	chr9:79306800-79307200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr9:79306800-79307200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr9:79306800-79307200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
50	chr9:79306800-79307200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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