Variant report

Variant	rs1108396
Chromosome Location	chr1:86651272-86651273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10747327	0.81[EUR][1000 genomes]
rs10873763	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1108394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161741	0.89[GIH][hapmap]
rs11161743	0.89[GIH][hapmap]
rs11161746	0.83[GIH][hapmap]
rs12075854	0.83[GIH][hapmap]
rs12117437	0.83[GIH][hapmap]
rs12120396	0.83[GIH][hapmap]
rs2039603	0.89[GIH][hapmap]
rs2135809	0.81[EUR][1000 genomes]
rs2390014	0.83[GIH][hapmap]
rs4655916	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6420970	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6576802	0.84[ASW][hapmap]
rs6576806	0.83[GIH][hapmap]
rs6576810	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6576814	0.83[EUR][1000 genomes]
rs6675364	0.89[GIH][hapmap]
rs71499360	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs74097323	0.92[EUR][1000 genomes]
rs7540048	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7550559	0.89[GIH][hapmap]
rs7550571	0.89[GIH][hapmap]
rs9432985	0.88[EUR][1000 genomes]
rs9432988	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9433431	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1108396	LOC339524	cis	parietal	SCAN
rs1108396	COL24A1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86648800-86652200	Enhancers	Fetal Lung	lung
2	chr1:86650400-86652800	Weak transcription	Ovary	ovary

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