Variant report

Variant	rs4394491
Chromosome Location	chr9:27092254-27092255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10738762	0.83[JPT][hapmap]
rs10757635	0.83[JPT][hapmap]
rs10812503	0.89[JPT][hapmap]
rs10812507	0.90[JPT][hapmap]
rs10812518	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10812521	0.82[AMR][1000 genomes]
rs10812523	0.82[AMR][1000 genomes]
rs10812525	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10967652	0.90[JPT][hapmap]
rs10967679	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs10967680	0.82[AMR][1000 genomes]
rs10967704	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10967706	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235354	0.82[ASN][1000 genomes]
rs12350647	0.86[ASN][1000 genomes]
rs1541144	0.90[JPT][hapmap]
rs1577328	0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1577330	0.85[ASN][1000 genomes]
rs1591355	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2095405	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2152062	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3758218	0.89[JPT][hapmap]
rs4412438	0.89[ASN][1000 genomes]
rs4463511	0.84[AMR][1000 genomes]
rs4621911	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs58336076	0.86[ASN][1000 genomes]
rs640282	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475954	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs6475955	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7018585	0.90[JPT][hapmap]
rs7020010	0.81[JPT][hapmap]
rs7030567	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7038218	0.94[JPT][hapmap]
rs7042447	0.84[JPT][hapmap]
rs7045747	0.80[AMR][1000 genomes]
rs7857669	0.83[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap]
rs7859996	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7860542	0.84[JPT][hapmap]
rs7863476	0.83[JPT][hapmap]
rs7870787	0.81[JPT][hapmap]
rs7871668	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4394491	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr9:27089600-27094000	Weak transcription	Fetal Kidney	kidney
3	chr9:27090200-27094000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:27090200-27094000	Weak transcription	NH-A	brain
5	chr9:27090600-27093800	Weak transcription	HSMMtube	muscle
6	chr9:27090600-27094000	Weak transcription	HSMM	muscle
7	chr9:27090800-27094000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:27090800-27094600	Weak transcription	NHLF	lung
9	chr9:27091000-27093800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:27091400-27093800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:27091600-27092600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:27091600-27092600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:27091600-27095800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:27092000-27093800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:27092200-27093800	Weak transcription	Osteobl	bone
16	chr9:27092200-27094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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