Variant report

Variant	rs498266
Chromosome Location	chr9:79306919-79306920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10512061	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11145009	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11145022	0.80[JPT][hapmap]
rs1536820	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2487263	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2553212	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2553213	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4745571	0.80[JPT][hapmap]
rs488165	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs489069	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs506965	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511545	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519983	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs520365	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs530978	0.83[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs537903	0.81[AFR][1000 genomes]
rs551262	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs557352	0.83[CEU][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs571960	0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs579025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs620985	0.87[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap]
rs625426	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630423	0.83[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs641088	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs677061	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684639	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs685011	0.83[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs700757	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs786597	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs498266	TMC1	cis	parietal	SCAN
rs498266	TLE4	cis	parietal	SCAN
rs498266	PRUNE2	cis	cerebellum	SCAN
rs498266	VPS13A	cis	parietal	SCAN
rs498266	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79304200-79307800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:79305000-79307600	Weak transcription	Aorta	Aorta
4	chr9:79305200-79307200	Enhancers	Colon Smooth Muscle	Colon
5	chr9:79305200-79307600	Enhancers	Stomach Mucosa	stomach
6	chr9:79306000-79307200	Active TSS	Brain Angular Gyrus	brain
7	chr9:79306000-79307200	Enhancers	Lung	lung
8	chr9:79306000-79307600	Active TSS	Fetal Brain Female	brain
9	chr9:79306000-79307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79306000-79307800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:79306000-79307800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr9:79306200-79307000	Active TSS	Fetal Thymus	thymus
13	chr9:79306400-79307200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:79306400-79307200	Enhancers	Colonic Mucosa	Colon
15	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr9:79306400-79307400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr9:79306400-79307400	Active TSS	Fetal Brain Male	brain
19	chr9:79306400-79307400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:79306600-79307000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr9:79306600-79307000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:79306600-79307000	Active TSS	Primary B cells from cord blood	blood
23	chr9:79306600-79307000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr9:79306600-79307000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:79306600-79307000	Enhancers	Liver	Liver
26	chr9:79306600-79307000	Active TSS	NHDF-Ad	bronchial
27	chr9:79306600-79307200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:79306600-79307200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr9:79306600-79307200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:79306600-79307200	Active TSS	Right Atrium	heart
31	chr9:79306600-79307400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr9:79306600-79307400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr9:79306600-79307400	Active TSS	Primary T cells from cord blood	blood
34	chr9:79306600-79307400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:79306600-79307400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:79306600-79307400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr9:79306600-79307400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr9:79306600-79307400	Flanking Active TSS	HUVEC	blood vessel
39	chr9:79306600-79307600	Flanking Active TSS	Osteobl	bone
40	chr9:79306600-79307800	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr9:79306600-79307800	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr9:79306600-79307800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr9:79306600-79308000	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr9:79306600-79308000	Enhancers	Gastric	stomach
45	chr9:79306800-79307000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:79306800-79307000	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:79306800-79307000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:79306800-79307000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
49	chr9:79306800-79307000	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr9:79306800-79307000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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