Variant report

Variant	rs2780103
Chromosome Location	chr9:86574568-86574569
allele	A/C/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	TCF12	chr9:86573745-86574580	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:86574383-86574752	HepG2	liver:	n/a	n/a
3	JUND	chr9:86573908-86574739	SK-N-SH	brain:	n/a	chr9:86574094-86574105

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86569929..86574114-chr9:86574225..86577710,5	MCF-7	breast:
2	chr9:86570737..86572270-chr9:86573976..86575561,2	K562	blood:

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

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10115699	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10125715	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10868068	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10868070	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10868071	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868076	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10868080	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11140251	0.88[CHB][hapmap]
rs11140253	0.88[CHB][hapmap]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140304	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12378956	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs12682981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13290882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes]
rs13295313	0.81[EUR][1000 genomes]
rs13296528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs167203	0.82[CEU][hapmap]
rs1831757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1889113	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982151	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2576362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521174	0.81[EUR][1000 genomes]
rs296883	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs296886	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs296887	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296888	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296889	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296890	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296892	0.82[YRI][hapmap]
rs296893	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3180887	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs3818725	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs4147132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535826	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4877814	0.82[YRI][hapmap]
rs6559751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559752	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6559753	0.82[YRI][hapmap]
rs6559756	0.82[YRI][hapmap]
rs696825	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7020300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7021189	0.82[YRI][hapmap]
rs7033292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7045126	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7853254	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7853377	0.82[CEU][hapmap]
rs7869321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7875011	0.82[YRI][hapmap]
rs796003	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs796004	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs796007	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9410888	0.88[CHB][hapmap]
rs963459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2780103	C9orf64	cis	multi-tissue	Pritchard
rs2780103	LOC440173	cis	parietal	SCAN

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	chr9:86572200-86576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:86572200-86577000	Weak transcription	HMEC	breast
6	chr9:86572200-86577200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:86572200-86579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:86572200-86581000	Weak transcription	Primary T cells from cord blood	blood
9	chr9:86572200-86581000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:86572200-86581200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:86572200-86581600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:86572200-86581800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:86572200-86582000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:86572200-86582000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:86572200-86584600	Weak transcription	Ovary	ovary
18	chr9:86572200-86586600	Weak transcription	Aorta	Aorta
19	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:86572400-86576800	Weak transcription	Placenta	Placenta
21	chr9:86572400-86577000	Weak transcription	Fetal Intestine Small	intestine
22	chr9:86572400-86577200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:86572400-86577200	Weak transcription	NH-A	brain
24	chr9:86572400-86580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:86572400-86580600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:86572400-86580800	Weak transcription	Primary B cells from cord blood	blood
27	chr9:86572400-86581000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:86572400-86581000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:86572400-86581000	Weak transcription	Brain Germinal Matrix	brain
30	chr9:86572400-86581200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:86572400-86581200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:86572400-86581200	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:86572400-86581200	Weak transcription	Fetal Thymus	thymus
34	chr9:86572400-86581200	Weak transcription	Left Ventricle	heart
35	chr9:86572400-86581200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:86572400-86581200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:86572400-86581400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:86572400-86581400	Weak transcription	GM12878-XiMat	blood
39	chr9:86572400-86581400	Weak transcription	HUVEC	blood vessel
40	chr9:86572400-86581600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:86572400-86581600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr9:86572400-86581800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:86572400-86581800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr9:86572400-86581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr9:86572400-86582000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:86572400-86582200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:86572400-86582200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:86572400-86582600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:86572400-86582600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:86572400-86584000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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