Variant report

Variant	rs28887790
Chromosome Location	chr16:47878394-47878395
allele	A/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:16)

rs_ID	r²[population]
rs12102942	0.89[AFR][1000 genomes]
rs1486419	0.86[AFR][1000 genomes]
rs1901903	0.81[AFR][1000 genomes]
rs28409782	0.81[AFR][1000 genomes]
rs28712810	0.92[AFR][1000 genomes]
rs28715928	0.84[AFR][1000 genomes]
rs7186530	0.89[AFR][1000 genomes]
rs7205736	0.83[AFR][1000 genomes]
rs728884	0.82[AFR][1000 genomes]
rs73536770	0.81[AFR][1000 genomes]
rs7500284	0.81[AFR][1000 genomes]
rs8064193	0.81[AFR][1000 genomes]
rs9927096	0.83[AFR][1000 genomes]
rs9927438	0.83[AFR][1000 genomes]
rs9934384	0.81[AFR][1000 genomes]
rs9934668	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520355	chr16:47424828-48164777	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv525976	chr16:47583872-48035026	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428657	chr16:47748036-47913816	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv833218	chr16:47869819-48051745	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv15547	chr16:47872598-47878432	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28887790	LOC388272	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47874800-47881400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:47877200-47880800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr16:47877200-47880800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr16:47877400-47880400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr16:47877400-47880600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:47877400-47881200	Weak transcription	H9 Cell Line	embryonic stem cell

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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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