Variant report

Variant	rs1572031
Chromosome Location	chr9:86571798-86571799
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	ZNF143	chr9:86571699-86572019	K562	blood:	n/a	n/a
2	POLR2A	chr9:86570895-86571974	GM12878	blood:	n/a	n/a
3	PML	chr9:86570857-86572016	GM12878	blood:	n/a	n/a
4	ZNF143	chr9:86571300-86571992	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr9:86571398-86571861	K562	blood:	n/a	n/a
6	PML	chr9:86571407-86571880	K562	blood:	n/a	n/a
7	UBTF	chr9:86571081-86572094	K562	blood:	n/a	n/a
8	EBF1	chr9:86570918-86571800	GM12878	blood:	n/a	n/a
9	GABPA	chr9:86571541-86571860	GM12878	blood:	n/a	n/a
10	MYC	chr9:86570808-86572117	K562	blood:	n/a	n/a
11	ZKSCAN1	chr9:86571260-86572044	Hela-S3	cervix:	n/a	n/a
12	YY1	chr9:86571461-86572151	SK-N-SH_RA	brain:	n/a	chr9:86571789-86571798
13	SRF	chr9:86571259-86571828	ECC-1	luminal epithelium:	n/a	chr9:86571590-86571608 chr9:86571592-86571609
14	POLR2A	chr9:86570841-86572067	GM12892	blood:	n/a	n/a
15	POLR2A	chr9:86571256-86572274	U87	brain:	n/a	n/a
16	EP300	chr9:86571198-86571894	HepG2	liver:	n/a	chr9:86571652-86571659
17	TAF1	chr9:86571275-86572064	K562	blood:	n/a	n/a
18	TAF1	chr9:86571372-86572054	HepG2	liver:	n/a	n/a
19	GABPA	chr9:86570998-86572207	MCF-7	breast:	n/a	n/a
20	MAX	chr9:86570867-86572232	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr9:86571351-86571910	SK-N-MC	brain:	n/a	n/a
22	MYC	chr9:86570990-86572004	K562	blood:	n/a	n/a
23	JUND	chr9:86571344-86571905	A549	lung:	n/a	n/a
24	MAX	chr9:86570818-86572270	HepG2	liver:	n/a	n/a
25	POLR2A	chr9:86570928-86571947	GM12891	blood:	n/a	n/a
26	TAF1	chr9:86571263-86571824	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr9:86570908-86572161	K562	blood:	n/a	n/a
28	POLR2A	chr9:86570840-86572132	K562	blood:	n/a	n/a
29	POLR2A	chr9:86570432-86572584	K562	blood:	n/a	n/a
30	POLR2A	chr9:86571173-86572131	PANC-1	pancreas:	n/a	n/a
31	ZNF384	chr9:86571135-86572132	K562	blood:	n/a	n/a
32	YY1	chr9:86570973-86572107	HepG2	liver:	n/a	chr9:86571789-86571798
33	MAX	chr9:86571229-86572289	MCF-7	breast:	n/a	n/a
34	POLR2A	chr9:86571053-86572087	MCF-7	breast:	n/a	n/a
35	NFIC	chr9:86571182-86571969	HepG2	liver:	n/a	n/a
36	POLR2A	chr9:86571024-86571924	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:86571169-86571955	HepG2	liver:	n/a	n/a
38	TAF1	chr9:86571022-86571885	HepG2	liver:	n/a	n/a
39	POLR2A	chr9:86570960-86572079	A549	lung:	n/a	n/a
40	MXI1	chr9:86571568-86572137	K562	blood:	n/a	chr9:86571820-86571829
41	SRF	chr9:86571380-86572077	ECC-1	luminal epithelium:	n/a	chr9:86571590-86571608 chr9:86571592-86571609
42	E2F6	chr9:86571304-86571992	H1-hESC	embryonic stem cell:	n/a	chr9:86571899-86571906 chr9:86571899-86571906 chr9:86571445-86571457 chr9:86571899-86571906
43	GTF2B	chr9:86571520-86571814	K562	blood:	n/a	n/a
44	POLR2A	chr9:86571403-86572032	A549	lung:	n/a	n/a
45	ELK1	chr9:86571400-86572040	Hela-S3	cervix:	n/a	chr9:86571704-86571713 chr9:86571704-86571713
46	POLR2A	chr9:86571018-86571856	GM12891	blood:	n/a	n/a
47	MAZ	chr9:86571074-86571875	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:86570946-86572090	Hela-S3	cervix:	n/a	n/a
49	YY1	chr9:86571368-86572174	ECC-1	luminal epithelium:	n/a	chr9:86571789-86571798
50	ZBTB7A	chr9:86570929-86572124	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:98922926..98923573-chr9:86571634..86572370,2	Hela-S3	cervix:
2	chr3:73159959..73160592-chr9:86571618..86572404,2	Hela-S3	cervix:
3	chr9:86534561..86538164-chr9:86570673..86573880,3	K562	blood:
4	chr9:86237033..86239481-chr9:86571525..86573399,2	MCF-7	breast:
5	chr9:86534003..86537844-chr9:86570557..86574103,8	K562	blood:
6	chr15:72410541..72411177-chr9:86571005..86571803,2	Hela-S3	cervix:
7	chr9:86534503..86538702-chr9:86568820..86574555,7	MCF-7	breast:

Variant related genes	Relation type
C9orf64	TF binding region
ENSG00000165115	Chromatin interaction
ENSG00000148057	Chromatin interaction
ENSG00000166192	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000066933	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10124390	0.87[CHB][hapmap]
rs10780638	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868058	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10868074	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868077	0.86[CHB][hapmap]
rs10868079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11140240	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11140323	0.85[EUR][1000 genomes]
rs11792634	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs12349272	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12551039	0.87[CHB][hapmap]
rs1572030	0.87[CHB][hapmap]
rs192705	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2065516	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][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];1.00[YRI][hapmap]
rs295291	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs296885	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]
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];0.93[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap]
rs4877814	0.83[CHB][hapmap]
rs4877815	0.83[CHB][hapmap]
rs6559750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6559753	0.83[CHB][hapmap]
rs6559754	0.87[CHB][hapmap]
rs6559756	0.83[CHB][hapmap]
rs7021189	0.87[CHB][hapmap]
rs7024316	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7026436	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs754144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855503	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7865878	0.85[ASN][1000 genomes]
rs7869387	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][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];0.96[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs796001	0.87[CHB][hapmap]
rs9314723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1572031	C9orf64	cis	parietal	SCAN
rs1572031	C9orf64	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86570200-86571800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:86570200-86572000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:86570400-86571800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr9:86570400-86572000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:86570400-86572000	Active TSS	HepG2	liver
6	chr9:86570400-86572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:86570400-86572200	Active TSS	Fetal Intestine Small	intestine
8	chr9:86570400-86572200	Active TSS	Psoas Muscle	Psoas
9	chr9:86570400-86572400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:86570400-86572400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr9:86570400-86572400	Active TSS	Right Ventricle	heart
12	chr9:86570400-86572400	Flanking Active TSS	NHEK	skin
13	chr9:86570400-86572600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:86570400-86572600	Active TSS	HSMMtube	muscle
15	chr9:86570600-86572000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:86570600-86572000	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr9:86570600-86572000	Active TSS	Thymus	Thymus
18	chr9:86570600-86572200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr9:86570600-86572200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr9:86570600-86572200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr9:86570600-86572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:86570600-86572200	Active TSS	HSMM	muscle
23	chr9:86570600-86572200	Active TSS	K562	blood
24	chr9:86570600-86572600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:86570800-86572000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:86570800-86572000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:86570800-86572000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:86570800-86572000	Active TSS	Fetal Lung	lung
29	chr9:86570800-86572000	Active TSS	Stomach Smooth Muscle	stomach
30	chr9:86570800-86572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:86570800-86572200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:86570800-86572200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:86570800-86572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:86570800-86572400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr9:86570800-86572400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:86570800-86572400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr9:86570800-86572400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:86570800-86572400	Active TSS	GM12878-XiMat	blood
39	chr9:86570800-86572600	Active TSS	Colonic Mucosa	Colon
40	chr9:86571000-86571800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
41	chr9:86571000-86572000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:86571000-86572000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr9:86571000-86572000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:86571000-86572000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:86571000-86572000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr9:86571000-86572000	Active TSS	Brain Hippocampus Middle	brain
47	chr9:86571000-86572000	Active TSS	Duodenum Mucosa	Duodenum
48	chr9:86571000-86572000	Active TSS	A549	lung
49	chr9:86571000-86572000	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr9:86571000-86572200	Active TSS	H1 Cell Line	embryonic stem cell

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