Variant report

Variant	rs12350647
Chromosome Location	chr9:27086205-27086206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10812525	0.80[ASN][1000 genomes]
rs10967704	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10967706	0.88[ASN][1000 genomes]
rs1577330	0.81[ASN][1000 genomes]
rs1591355	0.81[ASN][1000 genomes]
rs2095405	0.81[ASN][1000 genomes]
rs2152062	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4394491	0.86[ASN][1000 genomes]
rs4412438	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58336076	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs640282	0.85[ASN][1000 genomes]
rs6475955	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7024327	0.86[AFR][1000 genomes]
rs7030567	0.81[AMR][1000 genomes];0.81[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12350647	IFT74	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27024600-27086800	Weak transcription	Right Ventricle	heart
2	chr9:27024800-27094800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:27053800-27086800	Weak transcription	HSMM	muscle
4	chr9:27055200-27087000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:27068000-27087400	Weak transcription	Lung	lung
6	chr9:27072200-27087000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:27073000-27086800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:27076800-27087200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:27077600-27086800	Weak transcription	Fetal Stomach	stomach
10	chr9:27078600-27086800	Weak transcription	Fetal Heart	heart
11	chr9:27079800-27087600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr9:27081600-27087000	Weak transcription	Hela-S3	cervix
13	chr9:27082800-27086800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:27085200-27088000	Enhancers	Fetal Lung	lung
15	chr9:27085400-27087200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:27085400-27088000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:27085600-27086600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:27085600-27086800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:27085800-27087000	Weak transcription	Ovary	ovary

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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