Variant report

Variant	rs4147133
Chromosome Location	chr9:86559104-86559105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86557117..86561082-chr9:86568823..86572944,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165118	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125715	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10868068	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868070	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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];0.88[ASN][1000 genomes]
rs10868076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10868080	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140251	0.88[CHB][hapmap]
rs11140253	0.88[CHB][hapmap]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140304	1.00[CHB][hapmap];1.00[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];0.86[YRI][hapmap]
rs13290882	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13296528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs167203	0.82[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];0.82[ASN][1000 genomes]
rs1889113	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1982151	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2378661	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs2576362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780103	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]
rs296883	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[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];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296888	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296889	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296890	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296893	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3180887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs3818725	0.88[CHB][hapmap]
rs4147132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs4535826	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559751	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]
rs6559752	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs696825	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7020300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7045126	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7047907	0.94[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7853254	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7853377	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7869321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs796003	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs796004	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796007	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9410888	0.88[CHB][hapmap]
rs963459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4147133	C9orf64	cis	multi-tissue	Pritchard
rs4147133	LOC440173	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
3	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
5	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:86550200-86559200	Weak transcription	Brain Anterior Caudate	brain
7	chr9:86550200-86570400	Weak transcription	Aorta	Aorta
8	chr9:86550400-86569200	Weak transcription	Fetal Heart	heart
9	chr9:86550400-86570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:86550600-86559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:86550600-86569000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:86550800-86563800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:86550800-86568800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:86550800-86570400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:86551000-86559200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:86551000-86570400	Weak transcription	Stomach Mucosa	stomach
17	chr9:86551000-86570400	Weak transcription	NH-A	brain
18	chr9:86551600-86570000	Weak transcription	Fetal Brain Male	brain
19	chr9:86551600-86570200	Weak transcription	NHEK	skin
20	chr9:86552000-86562000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:86552000-86570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:86552000-86570400	Weak transcription	Spleen	Spleen
23	chr9:86552200-86559200	Weak transcription	HSMM	muscle
24	chr9:86552400-86559400	Strong transcription	Fetal Brain Female	brain
25	chr9:86552400-86560200	Strong transcription	Adipose Nuclei	Adipose
26	chr9:86552600-86559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:86552800-86560200	Strong transcription	HepG2	liver
28	chr9:86552800-86561800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:86553000-86559200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:86553000-86561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:86553000-86561800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:86553000-86570400	Weak transcription	Colonic Mucosa	Colon
33	chr9:86553200-86562200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:86553400-86559400	Strong transcription	Osteobl	bone
35	chr9:86553400-86562000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr9:86553400-86563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:86553600-86559400	Strong transcription	Fetal Thymus	thymus
38	chr9:86553600-86560200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:86553600-86560200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:86553600-86560200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:86553600-86560200	Strong transcription	Colon Smooth Muscle	Colon
42	chr9:86553600-86560400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:86553600-86560800	Strong transcription	Left Ventricle	heart
44	chr9:86553600-86561600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:86553600-86562000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:86553600-86562600	Strong transcription	Fetal Muscle Leg	muscle
47	chr9:86553600-86570000	Strong transcription	Fetal Stomach	stomach
48	chr9:86553800-86560000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr9:86553800-86560000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr9:86553800-86560200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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