Variant report

Variant	rs10493615
Chromosome Location	chr1:79180670-79180671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1107320	0.84[EUR][1000 genomes]
rs1109244	0.89[EUR][1000 genomes]
rs11162523	0.84[EUR][1000 genomes]
rs11162536	0.88[EUR][1000 genomes]
rs11162537	0.88[EUR][1000 genomes]
rs11162539	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162540	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162541	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162542	0.84[ASN][1000 genomes]
rs11162544	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587990	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120187	0.84[EUR][1000 genomes]
rs12128384	0.84[EUR][1000 genomes]
rs12403117	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406297	0.83[EUR][1000 genomes]
rs12406475	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12409331	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409781	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395034	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398682	0.86[EUR][1000 genomes]
rs17399158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399479	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17400419	0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs17400647	0.83[EUR][1000 genomes]
rs17400696	0.83[EUR][1000 genomes]
rs17400982	0.82[EUR][1000 genomes]
rs1780748	0.84[ASN][1000 genomes]
rs1887286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926901	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926902	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926903	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926904	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926905	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs273250	0.90[CEU][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs58150654	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58830966	0.84[EUR][1000 genomes]
rs58921479	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58945140	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58993850	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409549	0.84[EUR][1000 genomes]
rs60311076	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61500835	0.88[EUR][1000 genomes]
rs61613596	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61681700	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61768666	0.83[EUR][1000 genomes]
rs61769988	0.84[EUR][1000 genomes]
rs61769992	0.88[EUR][1000 genomes]
rs61769996	0.88[EUR][1000 genomes]
rs61770023	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770024	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424786	0.84[ASN][1000 genomes]
rs6678067	0.86[EUR][1000 genomes]
rs7546403	0.85[EUR][1000 genomes]
rs975986	0.84[EUR][1000 genomes]
rs975987	0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10493615	IFI44	cis	parietal	SCAN
rs10493615	ZZZ3	cis	cerebellum	SCAN
rs10493615	IFI44	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79178400-79184800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:79178400-79185000	Enhancers	Osteobl	bone
3	chr1:79179800-79183400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:79180000-79184600	Enhancers	NHDF-Ad	bronchial
5	chr1:79180200-79180800	Weak transcription	HSMMtube	muscle
6	chr1:79180200-79182400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:79180400-79181400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:79180400-79182000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:79180600-79180800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:79180600-79180800	Enhancers	Brain Germinal Matrix	brain
11	chr1:79180600-79181800	Enhancers	NHLF	lung
12	chr1:79180600-79182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:79180600-79184800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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