Variant report

Variant	rs1577404
Chromosome Location	chr13:80310771-80310772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1335293	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1414116	0.93[EUR][1000 genomes]
rs2027152	0.88[EUR][1000 genomes]
rs2039552	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2039553	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2095470	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329119	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2329120	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591027	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139876	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8001312	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9530951	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9545179	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9565521	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9574460	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1039333	chr13:80289936-80333167	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1577404	POU4F1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80309600-80311400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:80309600-80311600	Enhancers	HMEC	breast
3	chr13:80309800-80311600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:80309800-80324400	Weak transcription	Right Atrium	heart
5	chr13:80310000-80311400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:80310000-80311600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:80310000-80315000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:80310000-80315000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:80310000-80315000	Weak transcription	HSMM	muscle
10	chr13:80310200-80311400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:80310200-80311400	Enhancers	Esophagus	oesophagus
12	chr13:80310200-80311400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr13:80310200-80311400	Enhancers	NHEK	skin
14	chr13:80310200-80315200	Weak transcription	Left Ventricle	heart
15	chr13:80310400-80319400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:80310600-80315000	Weak transcription	HSMMtube	muscle

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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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