Variant report

Variant	rs62153923
Chromosome Location	chr2:97063603-97063604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12614188	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17633463	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2085842	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305935	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4907233	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907312	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56027554	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56221936	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153900	0.81[AMR][1000 genomes]
rs62153901	0.81[AMR][1000 genomes]
rs62153902	0.81[AMR][1000 genomes]
rs62153906	0.80[AFR][1000 genomes]
rs62153915	0.80[AMR][1000 genomes]
rs62153917	0.89[ASN][1000 genomes]
rs62153922	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62154786	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62154787	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737429	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6755877	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562544	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv3416952	chr2:97043127-97076830	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62153923	AC008268.2	cis	Thyroid	GTEx
rs62153923	CIAO1	cis	lung	GTEx
rs62153923	AC008268.2	cis	lung	GTEx
rs62153923	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62153923	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153923	AC008268.2	cis	Artery Tibial	GTEx
rs62153923	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153923	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97061800-97064000	Enhancers	Adipose Nuclei	Adipose
2	chr2:97061800-97064000	Enhancers	Placenta	Placenta
3	chr2:97062000-97065200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:97062400-97065400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:97062600-97065400	Weak transcription	Spleen	Spleen
6	chr2:97062800-97063800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:97063000-97073200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:97063200-97063800	Enhancers	Brain Hippocampus Middle	brain
9	chr2:97063200-97064000	Enhancers	Fetal Thymus	thymus
10	chr2:97063400-97063800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:97063400-97064400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr2:97063600-97063800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:97063600-97063800	Enhancers	Lung	lung
14	chr2:97063600-97065800	Weak transcription	Fetal Muscle Leg	muscle

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