Variant report

Variant	rs2062723
Chromosome Location	chr16:55697964-55697965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11076111	0.85[CHB][hapmap]
rs12232407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13333066	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1532701	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17247999	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17307096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17841327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28618083	0.96[ASN][1000 genomes]
rs28811645	0.90[ASN][1000 genomes]
rs747107	0.95[CHB][hapmap]
rs9937434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][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	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	nsv517827	chr16:55656355-55698027	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	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
rs2062723	SLC6A2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 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	chr16:55694200-55698400	Enhancers	Fetal Muscle Leg	muscle
6	chr16:55694200-55698400	Enhancers	Fetal Stomach	stomach
7	chr16:55695000-55699400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:55695200-55698200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:55695400-55699600	Enhancers	HMEC	breast
10	chr16:55695600-55703800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr16:55695800-55699400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:55696000-55699400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr16:55696400-55698200	Weak transcription	Esophagus	oesophagus
14	chr16:55696800-55698400	Weak transcription	Brain Substantia Nigra	brain
15	chr16:55697000-55698200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:55697200-55700200	Enhancers	HepG2	liver
17	chr16:55697400-55699000	Enhancers	Adipose Nuclei	Adipose
18	chr16:55697800-55698000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr16:55697800-55698400	Enhancers	Fetal Muscle Trunk	muscle
20	chr16:55697800-55699200	Enhancers	Brain Hippocampus Middle	brain

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