Variant report

Variant	rs296885
Chromosome Location	chr9:86584903-86584904
allele	C/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	POLR2A	chr9:86584430-86584962	U87	brain:	n/a	n/a
2	POLR2A	chr9:86584280-86584940	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:86584516-86585297	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
5	POLR2A	chr9:86584396-86584981	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:86584443-86585232	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr9:86584320-86587706	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:86583383-86585603	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:86584491-86585638	U87	brain:	n/a	n/a
10	POLR2A	chr9:86584885-86585273	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr9:86584435-86585325	GM12892	blood:	n/a	n/a
12	POLR2A	chr9:86584325-86587727	K562	blood:	n/a	n/a
13	POLR2A	chr9:86584241-86585402	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr9:86584479-86584923	GM12892	blood:	n/a	n/a
15	POLR2A	chr9:86584019-86593013	HepG2	liver:	n/a	n/a
16	POLR2A	chr9:86584487-86584991	U87	brain:	n/a	n/a
17	POLR2A	chr9:86579375-86587923	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:86584549-86584915	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:86584854-86585438	K562	blood:	n/a	n/a
20	POLR2A	chr9:86584379-86585320	GM12892	blood:	n/a	n/a
21	POLR2A	chr9:86584412-86585371	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:86584434-86585205	HepG2	liver:	n/a	n/a
23	POLR2A	chr9:86584178-86592956	GM12891	blood:	n/a	n/a
24	POLR2A	chr9:86584472-86585227	MCF-7	breast:	n/a	n/a
25	POLR2A	chr9:86584386-86586173	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000235298	TF binding region
MIR7-1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10124390	0.87[CHB][hapmap]
rs10780638	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868058	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10868074	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10868077	0.86[CHB][hapmap]
rs10868079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140323	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11792634	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12349272	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12551039	0.87[CHB][hapmap]
rs1572030	0.87[CHB][hapmap]
rs1572031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs192705	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065516	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs2780142	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs295274	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs295291	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs296891	0.87[CHB][hapmap]
rs296892	0.87[CHB][hapmap]
rs4297107	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs4877814	0.83[CHB][hapmap]
rs4877815	0.83[CHB][hapmap]
rs6559750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6559753	0.83[CHB][hapmap]
rs6559754	0.87[CHB][hapmap]
rs6559756	0.83[CHB][hapmap]
rs7021189	0.87[CHB][hapmap]
rs7024316	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7026436	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs754144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869387	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs7875011	0.87[CHB][hapmap]
rs7875289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs796001	0.87[CHB][hapmap]
rs9314723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs296885	C9orf64	cis	cerebellum	SCAN
rs296885	C9orf64	cis	parietal	SCAN
rs296885	C9orf64	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86572000-86586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:86572200-86586600	Weak transcription	Aorta	Aorta
3	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:86572400-86585800	Weak transcription	Pancreas	Pancrea
5	chr9:86572400-86586000	Weak transcription	Gastric	stomach
6	chr9:86572400-86586000	Weak transcription	Psoas Muscle	Psoas
7	chr9:86572400-86586000	Weak transcription	Right Ventricle	heart
8	chr9:86572400-86590000	Weak transcription	Right Atrium	heart
9	chr9:86572600-86585600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:86573200-86585800	Weak transcription	Lung	lung
11	chr9:86577600-86586400	Weak transcription	Esophagus	oesophagus
12	chr9:86577600-86586600	Weak transcription	Stomach Mucosa	stomach
13	chr9:86577800-86586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:86579000-86585800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:86580200-86585800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:86580600-86588600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:86580600-86590400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:86580600-86591400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:86580800-86586000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:86580800-86588400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr9:86580800-86588600	Strong transcription	Dnd41	blood
22	chr9:86580800-86589800	Strong transcription	HMEC	breast
23	chr9:86581000-86586800	Strong transcription	A549	lung
24	chr9:86581000-86587800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:86581000-86590000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:86581000-86591000	Strong transcription	Osteobl	bone
27	chr9:86581000-86591200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:86581000-86591200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr9:86581200-86588800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:86581200-86589600	Strong transcription	Liver	Liver
31	chr9:86581200-86589600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:86581200-86589800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:86581200-86590000	Strong transcription	Fetal Muscle Leg	muscle
34	chr9:86581200-86590400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:86581200-86591200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:86581200-86591200	Strong transcription	Adipose Nuclei	Adipose
37	chr9:86581200-86591200	Strong transcription	HSMM	muscle
38	chr9:86581200-86591400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:86581200-86591600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr9:86581200-86591800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:86581200-86591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:86581200-86591800	Strong transcription	HSMMtube	muscle
43	chr9:86581200-86592200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:86581200-86592200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:86581200-86592400	Strong transcription	Fetal Thymus	thymus
46	chr9:86581200-86593000	Strong transcription	Placenta	Placenta
47	chr9:86581400-86588400	Strong transcription	Fetal Intestine Large	intestine
48	chr9:86581400-86589800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:86581400-86589800	Strong transcription	Brain Anterior Caudate	brain
50	chr9:86581400-86589800	Strong transcription	HUVEC	blood vessel

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