Variant report

Variant	rs12237297
Chromosome Location	chr9:86576394-86576395
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	POLR2A	chr9:86576052-86576456	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:86575241-86578828	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:86576122-86576406	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:86575564-86576464	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86569929..86574114-chr9:86574225..86577710,5	MCF-7	breast:

Variant related genes	Relation type
C9orf64	TF binding region
ENSG00000165118	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10780645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10868067	0.93[EUR][1000 genomes]
rs11140252	1.00[CHB][hapmap]
rs11140254	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11140271	1.00[EUR][1000 genomes]
rs11140274	0.92[EUR][1000 genomes]
rs11140275	0.92[EUR][1000 genomes]
rs11140280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140288	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140290	0.86[EUR][1000 genomes]
rs11140291	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11140292	1.00[EUR][1000 genomes]
rs11140294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140296	1.00[EUR][1000 genomes]
rs11140308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140313	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140321	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140337	1.00[EUR][1000 genomes]
rs11140338	1.00[EUR][1000 genomes]
rs11531847	1.00[EUR][1000 genomes]
rs11533022	1.00[EUR][1000 genomes]
rs11533047	0.93[EUR][1000 genomes]
rs11535577	1.00[EUR][1000 genomes]
rs11559387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12056961	1.00[EUR][1000 genomes]
rs12235653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235969	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12237056	1.00[EUR][1000 genomes]
rs2017558	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73469392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73471357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969148	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9776332	0.93[EUR][1000 genomes]

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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86571800-86584600	Weak transcription	Spleen	Spleen
2	chr9:86572000-86577200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:86572000-86586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:86572200-86577000	Weak transcription	HMEC	breast
5	chr9:86572200-86577200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:86572200-86579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:86572200-86581000	Weak transcription	Primary T cells from cord blood	blood
8	chr9:86572200-86581000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:86572200-86581200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:86572200-86581600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:86572200-86581800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:86572200-86582000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:86572200-86582000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:86572200-86584600	Weak transcription	Ovary	ovary
17	chr9:86572200-86586600	Weak transcription	Aorta	Aorta
18	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:86572400-86576800	Weak transcription	Placenta	Placenta
20	chr9:86572400-86577000	Weak transcription	Fetal Intestine Small	intestine
21	chr9:86572400-86577200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:86572400-86577200	Weak transcription	NH-A	brain
23	chr9:86572400-86580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:86572400-86580600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:86572400-86580800	Weak transcription	Primary B cells from cord blood	blood
26	chr9:86572400-86581000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:86572400-86581000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:86572400-86581000	Weak transcription	Brain Germinal Matrix	brain
29	chr9:86572400-86581200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:86572400-86581200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:86572400-86581200	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:86572400-86581200	Weak transcription	Fetal Thymus	thymus
33	chr9:86572400-86581200	Weak transcription	Left Ventricle	heart
34	chr9:86572400-86581200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:86572400-86581200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:86572400-86581400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:86572400-86581400	Weak transcription	GM12878-XiMat	blood
38	chr9:86572400-86581400	Weak transcription	HUVEC	blood vessel
39	chr9:86572400-86581600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr9:86572400-86581600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr9:86572400-86581800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:86572400-86581800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr9:86572400-86581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr9:86572400-86582000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:86572400-86582200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr9:86572400-86582200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr9:86572400-86582600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:86572400-86582600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:86572400-86584000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr9:86572400-86584400	Weak transcription	Fetal Heart	heart

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