Variant report

Variant	rs17398682
Chromosome Location	chr1:79148288-79148289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:79148244-79149227	SK-N-SH	brain:	n/a	chr1:79149154-79149164

Variant related genes	Relation type
ENSG00000221683	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10493615	0.86[EUR][1000 genomes]
rs1107320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1109244	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11162523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162536	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162537	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162539	0.87[EUR][1000 genomes]
rs11162540	0.86[EUR][1000 genomes]
rs11162541	0.86[EUR][1000 genomes]
rs11162544	0.86[EUR][1000 genomes]
rs11587990	0.86[EUR][1000 genomes]
rs12120187	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12403117	0.87[EUR][1000 genomes]
rs12409331	0.87[EUR][1000 genomes]
rs12409781	0.87[EUR][1000 genomes]
rs17395034	0.87[EUR][1000 genomes]
rs17395097	0.86[EUR][1000 genomes]
rs17399158	0.86[EUR][1000 genomes]
rs17399192	0.86[EUR][1000 genomes]
rs1887286	0.86[EUR][1000 genomes]
rs1926897	0.85[EUR][1000 genomes]
rs1926898	0.85[EUR][1000 genomes]
rs1926901	0.89[EUR][1000 genomes]
rs1926902	0.87[EUR][1000 genomes]
rs1926903	0.87[EUR][1000 genomes]
rs1926904	0.87[EUR][1000 genomes]
rs1926905	0.87[EUR][1000 genomes]
rs273250	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58150654	0.87[EUR][1000 genomes]
rs58830966	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58921479	0.87[EUR][1000 genomes]
rs58945140	0.86[EUR][1000 genomes]
rs58993850	0.87[EUR][1000 genomes]
rs59409549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60311076	0.87[EUR][1000 genomes]
rs61500835	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613596	0.87[EUR][1000 genomes]
rs61681700	0.87[EUR][1000 genomes]
rs61769988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61769992	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770023	0.87[EUR][1000 genomes]
rs61770024	0.87[EUR][1000 genomes]
rs6678067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546403	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975987	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17398682	IFI44	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:79143600-79151200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:79148000-79148400	Enhancers	Osteobl	bone
4	chr1:79148000-79148600	Enhancers	NHDF-Ad	bronchial
5	chr1:79148000-79149000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:79148000-79149000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:79148000-79149200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:79148200-79148400	Enhancers	HMEC	breast
9	chr1:79148200-79148600	Enhancers	HSMM	muscle
10	chr1:79148200-79149000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:79148200-79149000	Enhancers	NHLF	lung
12	chr1:79148200-79149800	Enhancers	HUVEC	blood vessel

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