Variant report

Variant	rs12406475
Chromosome Location	chr1:79188382-79188383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10493615	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11162539	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162540	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162541	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162544	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11587990	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12403117	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12406297	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409331	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12409781	0.85[EUR][1000 genomes]
rs1620302	0.91[ASN][1000 genomes]
rs1625911	0.91[ASN][1000 genomes]
rs1629252	0.91[ASN][1000 genomes]
rs17395034	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17395097	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17399158	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17399192	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17399479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400419	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17400647	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17400696	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17400982	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1887286	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1926897	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1926898	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1926901	0.85[EUR][1000 genomes]
rs1926902	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1926903	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1926904	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1926905	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2767494	0.91[ASN][1000 genomes]
rs58150654	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58921479	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58945140	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58993850	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60311076	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61613596	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61681700	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61768666	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61770023	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61770024	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv871588	chr1:79164901-79214489	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12406475	IFI44	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79186800-79189400	Enhancers	NHDF-Ad	bronchial
2	chr1:79187200-79189600	Enhancers	Osteobl	bone
3	chr1:79187600-79189600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:79187800-79189000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:79187800-79189400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:79188000-79188800	Enhancers	HSMM	muscle
7	chr1:79188000-79188800	Weak transcription	HSMMtube	muscle

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