Variant report

Variant	rs1965716
Chromosome Location	chr5:54177511-54177512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10042734	0.90[EUR][1000 genomes]
rs10044930	0.87[ASN][1000 genomes]
rs10056452	0.84[EUR][1000 genomes]
rs10805469	0.80[EUR][1000 genomes]
rs10805470	0.90[EUR][1000 genomes]
rs10940431	0.86[EUR][1000 genomes]
rs10940432	0.86[EUR][1000 genomes]
rs10940434	0.86[EUR][1000 genomes]
rs11738151	0.86[EUR][1000 genomes]
rs11742711	0.84[EUR][1000 genomes]
rs12657845	0.84[EUR][1000 genomes]
rs1560165	0.87[EUR][1000 genomes]
rs1560166	0.87[EUR][1000 genomes]
rs17588816	0.90[EUR][1000 genomes]
rs1988528	0.96[ASN][1000 genomes]
rs1991498	0.97[ASN][1000 genomes]
rs2017082	0.85[EUR][1000 genomes]
rs2017318	1.00[ASN][1000 genomes]
rs2017540	1.00[ASN][1000 genomes]
rs2019005	0.87[EUR][1000 genomes]
rs2195392	0.86[EUR][1000 genomes]
rs2195393	0.87[EUR][1000 genomes]
rs2407758	0.94[ASN][1000 genomes]
rs28564901	0.84[EUR][1000 genomes]
rs2897758	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3916738	0.84[EUR][1000 genomes]
rs3935813	0.85[EUR][1000 genomes]
rs4074332	0.80[ASN][1000 genomes]
rs4242047	0.81[EUR][1000 genomes]
rs4315891	0.88[ASN][1000 genomes]
rs4373237	0.86[ASN][1000 genomes]
rs4407587	0.88[ASN][1000 genomes]
rs4446420	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4502767	0.87[EUR][1000 genomes]
rs4865586	0.87[ASN][1000 genomes]
rs4865587	0.87[ASN][1000 genomes]
rs4865879	0.93[EUR][1000 genomes]
rs4865880	0.86[EUR][1000 genomes]
rs4865882	0.86[EUR][1000 genomes]
rs4865883	1.00[ASN][1000 genomes]
rs734097	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737526	0.86[EUR][1000 genomes]
rs7708368	0.91[ASN][1000 genomes]
rs7709516	0.90[EUR][1000 genomes]
rs7734613	0.92[ASN][1000 genomes]
rs976645	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs981978	0.91[ASN][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:17 , 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	chr5:54174800-54178600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:54176000-54179200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:54176000-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:54176200-54178200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:54176600-54178400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:54176600-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:54176800-54178600	Enhancers	HMEC	breast
11	chr5:54177000-54177600	Enhancers	Osteobl	bone
12	chr5:54177200-54177800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:54177200-54178000	Enhancers	HSMM	muscle
14	chr5:54177400-54177800	Enhancers	NHEK	skin
15	chr5:54177400-54178600	Weak transcription	Esophagus	oesophagus
16	chr5:54177400-54178800	Weak transcription	Gastric	stomach
17	chr5:54177400-54179200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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