Variant report

Variant	rs10817532
Chromosome Location	chr9:116680136-116680137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10116566	0.81[YRI][hapmap]
rs10122390	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10123606	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10513222	0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10513223	0.89[CEU][hapmap];0.93[GIH][hapmap];0.81[YRI][hapmap]
rs10982000	0.82[LWK][hapmap];0.81[YRI][hapmap]
rs10982007	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12343628	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13290326	0.85[ASN][1000 genomes]
rs1330169	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1888161	0.91[CHB][hapmap]
rs2183364	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2418259	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2900568	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2900569	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35189176	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979295	0.85[CEU][hapmap]
rs4979296	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4979297	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4979298	0.89[CEU][hapmap]
rs7026176	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7029830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7038501	0.85[CEU][hapmap]
rs7046776	0.89[GIH][hapmap]
rs7047895	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7852787	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7853127	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855811	0.81[CEU][hapmap]
rs871806	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs871808	0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs882980	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs944180	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9942970	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9942975	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10817532	SLC46A2	cis	parietal	SCAN
rs10817532	MUSK	cis	parietal	SCAN
rs10817532	ZNF618	cis	cerebellum	SCAN
rs10817532	PALM2-AKAP2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116659400-116685400	Weak transcription	A549	lung
2	chr9:116666400-116683800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:116666600-116683000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:116667400-116684400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:116668000-116681800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:116669400-116683000	Weak transcription	Osteobl	bone
7	chr9:116669600-116690400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:116669800-116683600	Weak transcription	HUVEC	blood vessel
9	chr9:116672000-116682000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:116672600-116684800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:116672800-116681800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:116674600-116681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:116674600-116682000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:116674600-116690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:116674800-116681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:116675000-116680200	Weak transcription	Brain Germinal Matrix	brain
17	chr9:116675200-116681000	Weak transcription	Brain Angular Gyrus	brain
18	chr9:116675200-116684600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:116675400-116683200	Weak transcription	NHDF-Ad	bronchial
20	chr9:116675400-116684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:116675600-116680800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:116675600-116682000	Weak transcription	Brain Anterior Caudate	brain
23	chr9:116675600-116684000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:116675800-116680600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:116675800-116681000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:116675800-116681000	Weak transcription	Right Atrium	heart
27	chr9:116675800-116681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:116675800-116683400	Weak transcription	NHLF	lung
29	chr9:116675800-116683600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:116675800-116684600	Weak transcription	Esophagus	oesophagus
31	chr9:116675800-116686000	Weak transcription	Colonic Mucosa	Colon
32	chr9:116675800-116691800	Weak transcription	Lung	lung
33	chr9:116676000-116681400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:116676000-116682400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:116676000-116683200	Weak transcription	Gastric	stomach
36	chr9:116676000-116684800	Weak transcription	Fetal Kidney	kidney
37	chr9:116676200-116688000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:116676400-116681200	Weak transcription	Adipose Nuclei	Adipose
39	chr9:116676400-116684200	Weak transcription	HSMMtube	muscle
40	chr9:116676400-116685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:116676600-116682000	Weak transcription	Liver	Liver
42	chr9:116676800-116681000	Weak transcription	Aorta	Aorta
43	chr9:116677200-116681400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr9:116677400-116681200	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:116677600-116681000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:116677600-116681200	Weak transcription	Psoas Muscle	Psoas
47	chr9:116677600-116683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:116677800-116681000	Weak transcription	Ovary	ovary
49	chr9:116677800-116681000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:116677800-116681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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