Variant report

Variant	rs28844285
Chromosome Location	chr15:41879640-41879641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10438299	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1077714	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906912	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12915829	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246444	0.84[EUR][1000 genomes]
rs2277537	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482307	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28655000	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28792443	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784283	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924552	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924554	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924559	0.92[ASN][1000 genomes]
rs66906913	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68058196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7166371	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7183231	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025165	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28844285	MGA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41878000-41881000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41878200-41880600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:41878200-41882600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41878200-41882600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:41878200-41885600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:41878400-41882600	Weak transcription	HepG2	liver
7	chr15:41878400-41884600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:41878800-41883000	Enhancers	Placenta	Placenta
9	chr15:41878800-41885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:41879200-41881200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:41879200-41881200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:41879400-41880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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