Variant report

Variant	rs28501300
Chromosome Location	chr16:55704564-55704565
allele	A/G
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:13)

rs_ID	r²[population]
rs11076111	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13333066	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1362620	0.93[EUR][1000 genomes]
rs1362621	0.93[EUR][1000 genomes]
rs17307291	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242446	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2397771	0.91[ASN][1000 genomes]
rs28386840	0.90[EUR][1000 genomes]
rs28665972	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28693487	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3760019	0.93[EUR][1000 genomes]
rs3785147	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747107	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906673	chr16:55631035-55798370	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv431501	chr16:55639454-55789570	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2758426	chr16:55669396-55983590	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2758649	chr16:55669396-55983590	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28501300	SLC6A2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:55692600-55705400	Enhancers	Placenta	Placenta
2	chr16:55702800-55705600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:55703000-55706000	Weak transcription	Adipose Nuclei	Adipose
4	chr16:55703000-55731800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:55703600-55706000	Weak transcription	Fetal Muscle Leg	muscle
6	chr16:55703600-55706000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr16:55703600-55706000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr16:55703800-55708800	Weak transcription	Breast Myoepithelial Primary Cells	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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