Variant report

Variant	rs10967704
Chromosome Location	chr9:27088014-27088015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10757635	0.83[CHB][hapmap]
rs10812507	0.81[CHB][hapmap]
rs10812518	0.88[CHB][hapmap]
rs10812521	0.84[AMR][1000 genomes]
rs10812523	0.84[AMR][1000 genomes]
rs10812525	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10967679	0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[AMR][1000 genomes]
rs10967680	0.84[AMR][1000 genomes]
rs10967706	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1161603	0.80[TSI][hapmap]
rs12337896	0.81[JPT][hapmap]
rs12350647	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1577328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1577330	0.93[ASN][1000 genomes]
rs1591355	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1819539	0.88[JPT][hapmap]
rs2095405	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2152062	0.89[ASN][1000 genomes]
rs2225720	0.88[JPT][hapmap]
rs2991949	0.80[TSI][hapmap]
rs4394491	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4412438	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4463511	0.84[AMR][1000 genomes]
rs4621911	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs58336076	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs640282	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6475954	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6475955	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7030567	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7038218	0.83[CHB][hapmap]
rs7040505	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs7042447	0.83[CHB][hapmap]
rs7045747	0.83[AMR][1000 genomes]
rs7849248	0.82[CHB][hapmap]
rs7857669	0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[MEX][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes]
rs7859996	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7860542	0.83[CHB][hapmap]
rs7871668	0.82[CEU][hapmap];0.89[CHB][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs7872478	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10967704	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs10967704	IFT74	cis	lymphoblastoid	seeQTL
rs10967704	IFT74	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27024800-27094800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:27086600-27091000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr9:27086800-27090600	Enhancers	HSMM	muscle
4	chr9:27087000-27088800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:27087400-27088400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:27087400-27088800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:27087400-27090200	Enhancers	NH-A	brain
8	chr9:27087400-27092200	Enhancers	Osteobl	bone
9	chr9:27087800-27088800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:27087800-27088800	Weak transcription	HSMMtube	muscle
11	chr9:27087800-27089200	Weak transcription	Fetal Stomach	stomach
12	chr9:27087800-27089800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:27087800-27090800	Enhancers	NHLF	lung
14	chr9:27088000-27088800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:27088000-27089200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:27088000-27089200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:27088000-27089800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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