Variant report

Variant	rs882980
Chromosome Location	chr9:116683645-116683646
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10120883	0.85[CEU][hapmap]
rs10122390	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10123606	0.83[EUR][1000 genomes]
rs10448275	0.86[CHB][hapmap]
rs10513222	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513223	0.95[GIH][hapmap]
rs10817531	0.85[EUR][1000 genomes]
rs10817532	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]
rs10817535	0.81[EUR][1000 genomes]
rs10817539	0.86[CHB][hapmap]
rs10982007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12343628	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13290326	0.96[ASN][1000 genomes]
rs1330169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1888161	1.00[CHB][hapmap]
rs2065184	0.87[EUR][1000 genomes]
rs2183364	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2900568	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900569	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35189176	0.83[EUR][1000 genomes]
rs4979294	0.83[EUR][1000 genomes]
rs4979295	0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4979297	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs4979298	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7026176	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7029830	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7038501	0.96[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7046776	0.86[CHB][hapmap];0.91[GIH][hapmap]
rs7047895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7852787	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7853127	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855811	0.92[CEU][hapmap]
rs7867998	0.86[CHB][hapmap]
rs871806	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs871808	0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs944180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9942970	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9942975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs882980	ZNF618	cis	cerebellum	SCAN
rs882980	SLC46A2	cis	parietal	SCAN
rs882980	PALM2-AKAP2	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

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	chr9:116667400-116684400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:116669600-116690400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:116672600-116684800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:116674600-116690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:116675200-116684600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:116675400-116684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:116675600-116684000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:116675800-116684600	Weak transcription	Esophagus	oesophagus
11	chr9:116675800-116686000	Weak transcription	Colonic Mucosa	Colon
12	chr9:116675800-116691800	Weak transcription	Lung	lung
13	chr9:116676000-116684800	Weak transcription	Fetal Kidney	kidney
14	chr9:116676200-116688000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:116676400-116684200	Weak transcription	HSMMtube	muscle
16	chr9:116676400-116685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:116679200-116684400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:116679200-116689600	Weak transcription	HSMM	muscle
19	chr9:116679400-116686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:116679400-116691600	Weak transcription	Pancreas	Pancrea
21	chr9:116681000-116684000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:116681200-116683800	Enhancers	Psoas Muscle	Psoas
23	chr9:116681800-116683800	Strong transcription	Fetal Stomach	stomach
24	chr9:116682000-116684800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:116682400-116683800	Weak transcription	Aorta	Aorta
26	chr9:116682400-116684400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:116682400-116684600	Weak transcription	Spleen	Spleen
28	chr9:116682400-116692000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:116682600-116684000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:116683000-116684400	Enhancers	Osteobl	bone
31	chr9:116683200-116683800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:116683200-116684000	Enhancers	NHDF-Ad	bronchial
33	chr9:116683200-116684400	Weak transcription	Liver	Liver
34	chr9:116683400-116684000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:116683600-116683800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:116683600-116683800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:116683600-116683800	Enhancers	Placenta	Placenta
38	chr9:116683600-116684000	Weak transcription	NHLF	lung
39	chr9:116683600-116684200	Enhancers	HUVEC	blood vessel

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