Variant report

Variant	rs6559751
Chromosome Location	chr9:86551269-86551270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86549593..86551703-chr9:86556254..86557805,2	MCF-7	breast:
2	chr9:86534561..86538761-chr9:86547777..86551990,5	MCF-7	breast:
3	chr9:86548981..86555040-chr9:86588754..86596573,13	MCF-7	breast:
4	chr9:86550607..86552795-chr9:86930808..86933198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178966	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10115699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125715	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10868068	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868070	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868071	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10868076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10868080	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140251	0.87[CHB][hapmap]
rs11140253	0.87[CHB][hapmap]
rs11140265	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11140304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12378956	0.94[CHB][hapmap]
rs12682981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs13290882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13296528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs167203	0.83[CEU][hapmap]
rs1831757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1889113	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1982151	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2378661	0.94[CHB][hapmap]
rs2576362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780103	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]
rs296883	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs296886	0.82[CEU][hapmap]
rs296887	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs296888	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs296889	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs296890	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs296893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3180887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3818725	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs4147132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4535826	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559752	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs696825	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7020300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7045126	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047907	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7853254	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7853377	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7869321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs796003	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796004	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs796007	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9410888	0.87[CHB][hapmap]
rs963459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559751	C9orf64	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
4	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
5	chr9:86544000-86552400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:86546800-86553400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:86546800-86553600	Weak transcription	Fetal Thymus	thymus
8	chr9:86547200-86553600	Weak transcription	Primary T cells from cord blood	blood
9	chr9:86547200-86553800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr9:86547800-86554200	Weak transcription	Dnd41	blood
12	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
13	chr9:86548600-86551800	Enhancers	NHDF-Ad	bronchial
14	chr9:86548600-86551800	Enhancers	Osteobl	bone
15	chr9:86548600-86552000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:86548600-86552600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:86548600-86552600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:86548600-86553000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:86548800-86554400	Weak transcription	Small Intestine	intestine
20	chr9:86549000-86553800	Weak transcription	Pancreas	Pancrea
21	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:86549400-86553000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:86549600-86552400	Weak transcription	Fetal Brain Female	brain
24	chr9:86549600-86553600	Weak transcription	Liver	Liver
25	chr9:86549600-86553600	Weak transcription	Fetal Stomach	stomach
26	chr9:86549600-86553600	Weak transcription	Left Ventricle	heart
27	chr9:86549600-86557000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:86549800-86552000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr9:86550000-86552800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:86550200-86551400	Weak transcription	Gastric	stomach
31	chr9:86550200-86552200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:86550200-86552400	Weak transcription	Adipose Nuclei	Adipose
33	chr9:86550200-86552400	Weak transcription	Fetal Intestine Large	intestine
34	chr9:86550200-86552400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:86550200-86552600	Enhancers	Hela-S3	cervix
36	chr9:86550200-86552800	Weak transcription	HepG2	liver
37	chr9:86550200-86553400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:86550200-86553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:86550200-86553600	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:86550200-86553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:86550200-86553800	Weak transcription	Ovary	ovary
42	chr9:86550200-86553800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr9:86550200-86554000	Weak transcription	Lung	lung
44	chr9:86550200-86554000	Weak transcription	Right Ventricle	heart
45	chr9:86550200-86554400	Weak transcription	HSMMtube	muscle
46	chr9:86550200-86555000	Weak transcription	A549	lung
47	chr9:86550200-86555600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:86550200-86557000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:86550200-86557200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr9:86550200-86559200	Weak transcription	Brain Anterior Caudate	brain

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