Variant report

Variant	rs597673
Chromosome Location	chr1:209994012-209994013
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11579771	0.88[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs2236906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3753516	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs583814	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585191	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs593543	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596731	0.93[EUR][1000 genomes]
rs599021	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599663	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615276	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623360	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs632305	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs648349	0.94[ASN][1000 genomes]
rs651141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661755	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs684083	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs846808	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs861019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs597673	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209989600-209996000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:209991000-209994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:209991200-209994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209991200-209994200	Weak transcription	NHEK	skin
5	chr1:209991600-209996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:209992600-210000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209993200-209996000	Weak transcription	Fetal Intestine Large	intestine
8	chr1:209993400-209994400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:209993400-209999000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:209993600-209994200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:209994000-209994800	Enhancers	HMEC	breast

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

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