Variant report

Variant	rs1560168
Chromosome Location	chr5:54176846-54176847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10037462	1.00[AMR][1000 genomes]
rs10045193	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10051233	0.82[AFR][1000 genomes]
rs10065443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10075204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10075516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213818	1.00[AMR][1000 genomes]
rs13353863	1.00[AMR][1000 genomes]
rs13356362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13359248	1.00[AMR][1000 genomes]
rs16883502	0.82[AFR][1000 genomes]
rs28585462	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6861370	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6862424	1.00[AMR][1000 genomes]
rs6880497	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7708519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:54173200-54178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:54174400-54179000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:54174600-54177000	Weak transcription	Osteobl	bone
5	chr5:54174800-54178600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:54175800-54177000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:54175800-54177000	Enhancers	NHEK	skin
8	chr5:54176000-54179200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:54176000-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:54176200-54178200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:54176600-54178400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:54176600-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:54176800-54178600	Enhancers	HMEC	breast

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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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