Variant report

Variant	rs17650044
Chromosome Location	chr9:8482778-8482779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10117042	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10120190	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10123125	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10123138	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs10124867	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10217685	0.80[CEU][hapmap]
rs10511499	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10758979	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10758980	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10815883	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815889	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10815890	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10815891	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs10815896	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10815906	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10815907	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10815908	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10977142	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10977146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10977169	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs10977170	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10977181	0.83[JPT][hapmap]
rs12340211	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs12341045	0.81[ASN][1000 genomes]
rs12341078	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12344975	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs12683581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998513	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1998515	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2273998	0.83[JPT][hapmap]
rs2281747	0.93[MEX][hapmap]
rs3763652	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs3763653	0.83[JPT][hapmap]
rs55663135	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6477313	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7019398	0.81[CEU][hapmap]
rs7025468	0.95[CEU][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7858815	0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs7862199	0.93[MEX][hapmap]
rs7868790	1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17650044	C9orf46	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
3	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
4	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8442200-8522200	Weak transcription	Liver	Liver
6	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
8	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:8468600-8484000	Weak transcription	Ovary	ovary
11	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
12	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:8474000-8484000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8474400-8484800	Weak transcription	Fetal Heart	heart
15	chr9:8474400-8485200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:8475400-8483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:8475600-8483400	Weak transcription	Brain Substantia Nigra	brain
18	chr9:8476400-8483400	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:8476400-8483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:8477600-8485000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:8478000-8484000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:8478800-8483800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:8478800-8485000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:8478800-8485800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:8479000-8482800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:8479200-8483800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr9:8479400-8485200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:8480400-8483800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr9:8480400-8484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:8480600-8483800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr9:8480600-8484000	Weak transcription	Brain Anterior Caudate	brain
39	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:8481600-8488200	Strong transcription	Fetal Lung	lung
41	chr9:8482200-8482800	Strong transcription	Fetal Brain Female	brain
42	chr9:8482200-8483000	Strong transcription	Brain Germinal Matrix	brain
43	chr9:8482200-8486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:8482200-8487000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr9:8482600-8483000	Strong transcription	Dnd41	blood
47	chr9:8482600-8483400	Weak transcription	Fetal Brain Male	brain
48	chr9:8482600-8486000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:8482600-8486200	Strong transcription	Rectal Mucosa Donor 29	rectum

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