Variant report

Variant	rs17466389
Chromosome Location	chr15:49107640-49107641
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10775138	1.00[ASW][hapmap]
rs12899937	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902606	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12906456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12909029	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1426199	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17382306	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17382534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17383295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17383671	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs17468155	0.87[MKK][hapmap]
rs2899424	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34026160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34780506	0.87[ASN][1000 genomes]
rs35744700	1.00[ASN][1000 genomes]
rs4482220	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs62009451	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833001	chr15:49043643-49204765	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17466389	DUOXA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49104000-49124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:49104200-49112200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:49104200-49113400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:49104200-49115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:49104200-49115400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:49104400-49117000	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:49104400-49121200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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