Variant report

Variant	rs2462965
Chromosome Location	chr17:38863536-38863537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1012388	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078950	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11650910	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11869540	0.84[EUR][1000 genomes]
rs1474454	0.80[EUR][1000 genomes]
rs1526601	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16966093	0.80[EUR][1000 genomes]
rs1961204	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011870	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272288	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429547	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2429548	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2429550	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429551	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2462957	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462960	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462961	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462966	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462967	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462969	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469817	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469819	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469820	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469825	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55664118	0.80[EUR][1000 genomes]
rs6503545	0.80[EUR][1000 genomes]
rs6503546	0.80[EUR][1000 genomes]
rs67138687	0.80[EUR][1000 genomes]
rs723728	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723729	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726849	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065040	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8074758	0.83[EUR][1000 genomes]
rs874889	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887376	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9303294	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9630729	0.80[EUR][1000 genomes]
rs9675112	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
2	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2462965	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2462965	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2462965	KRT24	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38853400-38864000	Weak transcription	A549	lung
2	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
3	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:38856800-38863600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:38860000-38864000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:38860000-38864600	Weak transcription	Placenta	Placenta
7	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:38861600-38864200	Enhancers	Hela-S3	cervix
9	chr17:38861800-38864600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:38862000-38863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:38862200-38864200	Weak transcription	HMEC	breast
12	chr17:38862400-38864000	Weak transcription	NHEK	skin
13	chr17:38862600-38863600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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