Variant report

Variant	rs28754340
Chromosome Location	chr15:60016301-60016302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1979423	0.86[EUR][1000 genomes]
rs28478168	0.81[EUR][1000 genomes]
rs62012499	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7169509	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28754340	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60015000-60017200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:60016000-60016400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:60016200-60016600	Enhancers	Psoas Muscle	Psoas
4	chr15:60016200-60016800	Enhancers	A549	lung
5	chr15:60016200-60017200	Enhancers	Placenta	Placenta
6	chr15:60016200-60017600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:60016200-60017600	Flanking Active TSS	Hela-S3	cervix

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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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