Variant report

Variant	rs1998513
Chromosome Location	chr9:8508015-8508016
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10117042	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120190	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs10123125	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10123138	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10124867	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10217685	0.87[LWK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10511499	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10758978	0.85[ASN][1000 genomes]
rs10758979	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10758980	0.86[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10815883	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10815890	0.80[ASN][1000 genomes]
rs10815896	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10815898	0.85[ASN][1000 genomes]
rs10815900	0.86[GIH][hapmap]
rs10815905	0.80[ASN][1000 genomes]
rs10815906	0.86[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10815907	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10815908	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10977146	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10977169	0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10977170	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10977181	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10977189	0.81[ASN][1000 genomes]
rs12340211	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12341045	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12341078	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12344975	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12683581	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12686431	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17650044	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1998515	0.94[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273998	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs3763652	0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs3763653	0.85[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs55663135	0.84[ASN][1000 genomes]
rs6477313	1.00[CEU][hapmap];0.93[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];0.97[ASN][1000 genomes]
rs7019398	0.89[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7864841	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][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	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
6	nsv892229	chr9:8485201-8520366	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv613290	chr9:8501698-8514338	Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1998513	C9orf46	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8442200-8522200	Weak transcription	Liver	Liver
3	chr9:8483800-8524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:8486000-8508400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:8486000-8519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:8486000-8522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:8486200-8509000	Weak transcription	Brain Anterior Caudate	brain
8	chr9:8486200-8517200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:8486200-8522800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:8486200-8523200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
12	chr9:8487000-8521200	Weak transcription	Brain Germinal Matrix	brain
13	chr9:8487000-8521200	Weak transcription	Dnd41	blood
14	chr9:8492400-8528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:8493000-8518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:8493000-8521200	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:8493200-8523200	Weak transcription	Fetal Stomach	stomach
18	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
19	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
20	chr9:8495000-8517800	Weak transcription	Ovary	ovary
21	chr9:8495600-8520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:8499800-8517600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:8500600-8516800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:8501000-8509000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:8501000-8517600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:8501200-8517200	Weak transcription	Fetal Lung	lung
27	chr9:8501600-8517000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:8504200-8509200	Weak transcription	Brain Angular Gyrus	brain
29	chr9:8504400-8509000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:8504400-8509400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:8507000-8508800	Enhancers	Brain Substantia Nigra	brain
32	chr9:8507200-8508800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:8507200-8509000	Weak transcription	Brain Hippocampus Middle	brain

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