Variant report

Variant	rs3739524
Chromosome Location	chr9:79320095-79320096
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:79320040-79320190	HCPEpiC	choroid plexus:	n/a	n/a
2	REST	chr9:79319609-79320208	HL-60	blood:	n/a	n/a
3	CTCF	chr9:79320000-79320150	HPF	lung:	n/a	n/a
4	CTCF	chr9:79319353-79320142	SK-N-SH	brain:	n/a	n/a
5	REST	chr9:79319599-79320108	MCF-7	breast:	n/a	n/a
6	CTCF	chr9:79319980-79320130	HPF	lung:	n/a	n/a
7	CTCF	chr9:79319960-79320110	WI-38	lung:	n/a	n/a
8	REST	chr9:79319798-79320148	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr9:79319317-79320447	A549	lung:	n/a	n/a
10	SMC3	chr9:79319299-79320226	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr9:79319960-79320110	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr9:79319960-79320110	GM12865	blood:	n/a	n/a
13	CTCF	chr9:79320020-79320170	GM12868	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:79062552..79063515-chr9:79319220..79320201,4	K562	blood:
2	chr8:128943460..128943995-chr9:79320014..79320514,2	MCF-7	breast:
3	chr9:79017921..79018920-chr9:79318594..79320251,5	K562	blood:
4	chr9:79280331..79281278-chr9:79319093..79320181,5	MCF-7	breast:
5	chr9:79280654..79281415-chr9:79319254..79320174,3	K562	blood:
6	chr9:79281569..79282479-chr9:79319831..79320484,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000265488	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10781370	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10781371	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869798	0.90[ASN][1000 genomes]
rs10869800	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869801	0.81[AMR][1000 genomes]
rs10869805	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11145011	0.97[ASN][1000 genomes]
rs11145012	0.98[ASN][1000 genomes]
rs11145017	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145018	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145019	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11145021	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11145023	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12238013	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12683741	0.81[ASN][1000 genomes]
rs1329014	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536820	0.82[MEX][hapmap]
rs2077181	0.92[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277155	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3739521	0.92[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs537903	0.81[ASN][1000 genomes]
rs57608282	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs577993	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs600859	0.81[ASN][1000 genomes]
rs626837	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs641088	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs658548	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs683866	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7042953	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9314853	0.83[ASN][1000 genomes]
rs9785303	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv2754389	chr9:79318677-79333056	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3739524	PRUNE2	cis	cerebellum	SCAN
rs3739524	VPS13A	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:79317600-79330800	Strong transcription	HSMM	muscle
13	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
14	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:79318800-79323200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:79319400-79320200	Enhancers	Colon Smooth Muscle	Colon
18	chr9:79319800-79320200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:79319800-79320200	Enhancers	Brain Substantia Nigra	brain
20	chr9:79319800-79320200	Enhancers	Fetal Stomach	stomach
21	chr9:79319800-79320200	Bivalent Enhancer	HUVEC	blood vessel
22	chr9:79319800-79320400	Genic enhancers	Stomach Smooth Muscle	stomach
23	chr9:79319800-79320800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr9:79320000-79320200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:79320000-79320200	Bivalent Enhancer	Fetal Thymus	thymus
26	chr9:79320000-79321000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:79320000-79321000	Weak transcription	Fetal Brain Male	brain
28	chr9:79320000-79322800	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:79320000-79328000	Strong transcription	Aorta	Aorta
30	chr9:79320000-79328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
32	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain

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