Variant report

Variant	rs28693487
Chromosome Location	chr16:55698911-55698912
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:13)

rs_ID	r²[population]
rs11076111	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13333066	0.97[EUR][1000 genomes]
rs1362620	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1362621	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17307291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242446	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2397771	0.92[ASN][1000 genomes]
rs28386840	0.89[EUR][1000 genomes]
rs28501300	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28665972	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3760019	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3785147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747107	0.97[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
rs28693487	SLC6A2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:55692600-55705400	Enhancers	Placenta	Placenta
2	chr16:55693600-55699400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr16:55693600-55699400	Enhancers	NHEK	skin
4	chr16:55693800-55699000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:55695000-55699400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:55695400-55699600	Enhancers	HMEC	breast
7	chr16:55695600-55703800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr16:55695800-55699400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:55696000-55699400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr16:55697200-55700200	Enhancers	HepG2	liver
11	chr16:55697400-55699000	Enhancers	Adipose Nuclei	Adipose
12	chr16:55697800-55699200	Enhancers	Brain Hippocampus Middle	brain
13	chr16:55698000-55700200	Enhancers	Pancreas	Pancrea
14	chr16:55698200-55700200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:55698400-55702200	Weak transcription	Fetal Muscle Leg	muscle
16	chr16:55698800-55699000	Enhancers	H1 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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