Variant report

Variant	rs9942975
Chromosome Location	chr9:116689362-116689363
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10120883	0.85[CEU][hapmap]
rs10122390	0.89[CEU][hapmap]
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];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10513223	0.95[GIH][hapmap]
rs10817531	0.81[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];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817535	0.85[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];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12343628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13290326	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1330169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888161	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2065184	0.83[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];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2900568	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979295	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs4979297	0.89[CEU][hapmap]
rs4979298	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7026176	0.85[CEU][hapmap]
rs7029830	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7038501	0.96[CEU][hapmap];0.93[TSI][hapmap]
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];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7852787	0.89[CEU][hapmap]
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];0.82[EUR][1000 genomes];0.86[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];0.96[ASN][1000 genomes]
rs871808	0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs882980	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]
rs944180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9942970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs9942975	PALM2-AKAP2	cis	parietal	SCAN
rs9942975	SLC46A2	cis	parietal	SCAN
rs9942975	ZNF618	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116669600-116690400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:116674600-116690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:116675800-116691800	Weak transcription	Lung	lung
4	chr9:116679200-116689600	Weak transcription	HSMM	muscle
5	chr9:116679400-116691600	Weak transcription	Pancreas	Pancrea
6	chr9:116682400-116692000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:116684800-116690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:116684800-116690800	Weak transcription	Osteobl	bone
9	chr9:116686000-116689400	Weak transcription	Fetal Kidney	kidney
10	chr9:116686000-116691400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:116686000-116692000	Weak transcription	Fetal Heart	heart
12	chr9:116686600-116689400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:116688800-116689600	Weak transcription	HUVEC	blood vessel

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