Variant report

Variant	rs640282
Chromosome Location	chr9:27097030-27097031
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10738762	0.83[JPT][hapmap]
rs10757635	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10812503	0.89[JPT][hapmap]
rs10812507	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10812518	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10812525	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10967652	0.89[JPT][hapmap]
rs10967679	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10967704	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10967706	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1161603	0.87[TSI][hapmap]
rs12235354	0.81[ASN][1000 genomes]
rs12350647	0.85[ASN][1000 genomes]
rs1541144	0.89[JPT][hapmap]
rs1577328	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1577330	0.84[ASN][1000 genomes]
rs1591355	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2095405	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2152062	0.86[ASN][1000 genomes]
rs2991949	0.86[TSI][hapmap]
rs3758218	0.89[JPT][hapmap]
rs4394491	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4412438	0.87[ASN][1000 genomes]
rs4413873	0.81[JPT][hapmap]
rs4621911	0.82[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs58336076	0.84[ASN][1000 genomes]
rs6475954	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs6475955	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7018585	0.89[JPT][hapmap]
rs7030567	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7040505	0.82[CHB][hapmap]
rs7849248	0.82[CHB][hapmap]
rs7857669	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7859996	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7860542	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7863476	0.83[JPT][hapmap]
rs7871668	0.82[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7875068	0.89[JPT][hapmap]

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	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs640282	IFT74	cis	lymphoblastoid	seeQTL
rs640282	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs640282	IFT74	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27095200-27098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:27095200-27108800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:27095600-27102200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:27095600-27108800	Weak transcription	NH-A	brain
5	chr9:27096800-27109000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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