Variant report

Variant	rs7875289
Chromosome Location	chr9:86517190-86517191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10124390	0.86[CHB][hapmap]
rs10868058	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs10868074	0.84[ASN][1000 genomes]
rs10868077	0.86[CHB][hapmap]
rs10868079	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11140240	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11792634	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs12349272	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12377335	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12551039	0.87[CHB][hapmap]
rs1572030	0.87[CHB][hapmap]
rs1572031	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]
rs192705	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2065516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2780142	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs295275	0.85[EUR][1000 genomes]
rs295291	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs296885	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs296891	0.87[CHB][hapmap]
rs296892	0.87[CHB][hapmap]
rs3119753	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4297107	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs4877814	0.82[CHB][hapmap]
rs4877815	0.82[CHB][hapmap]
rs6559750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6559753	0.82[CHB][hapmap]
rs6559754	0.87[CHB][hapmap]
rs6559756	0.82[CHB][hapmap]
rs7021189	0.87[CHB][hapmap]
rs7024316	0.84[ASN][1000 genomes]
rs7026436	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[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];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs754144	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs7855503	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7865878	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7875011	0.87[CHB][hapmap]
rs796001	0.87[CHB][hapmap]
rs9314723	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	esv2753071	chr9:86500946-86517546	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv972407	chr9:86501897-86517820	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3451136	chr9:86514032-86517530	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
10	esv1794308	chr9:86514455-86517543	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv1804558	chr9:86514455-86517543	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	nsv442559	chr9:86514455-86517543	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7875289	C9orf64	cis	cerebellum	SCAN
rs7875289	GKAP1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
2	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86461600-86535400	Weak transcription	Ovary	ovary
4	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
5	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
7	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach
8	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:86482000-86518000	Weak transcription	Left Ventricle	heart
10	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:86491400-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:86491800-86518200	Weak transcription	Primary B cells from cord blood	blood
14	chr9:86495000-86518000	Weak transcription	Primary T cells from cord blood	blood
15	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:86496400-86533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:86499400-86518200	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:86499400-86535000	Weak transcription	Fetal Kidney	kidney
19	chr9:86499800-86523200	Weak transcription	Fetal Thymus	thymus
20	chr9:86500000-86534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:86500200-86521200	Weak transcription	Adipose Nuclei	Adipose
22	chr9:86500200-86521200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:86500200-86535200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:86500200-86535200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:86500200-86535600	Weak transcription	Lung	lung
26	chr9:86501200-86521600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:86502000-86532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:86502600-86535000	Weak transcription	Fetal Lung	lung
29	chr9:86503000-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:86506400-86534800	Weak transcription	Pancreas	Pancrea
31	chr9:86508200-86518400	Weak transcription	Aorta	Aorta
32	chr9:86508200-86535600	Weak transcription	Esophagus	oesophagus
33	chr9:86508400-86520200	Weak transcription	Liver	Liver
34	chr9:86509000-86521200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:86512400-86535400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:86512600-86518000	Weak transcription	Spleen	Spleen
37	chr9:86512600-86535400	Weak transcription	Placenta	Placenta
38	chr9:86513200-86534800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:86513800-86518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:86513800-86519000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:86516200-86521400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:86516200-86535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:86516400-86517800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:86517000-86519800	Weak transcription	Brain Cingulate Gyrus	brain

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