Variant report

Variant	rs12075854
Chromosome Location	chr1:86578951-86578952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11161736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161738	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161741	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161743	0.95[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161744	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161745	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024954	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048574	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12057841	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057874	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057993	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062793	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12117437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117849	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118936	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12120396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126086	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12567887	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1507266	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1507284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1507292	0.81[GIH][hapmap]
rs1948962	0.80[GIH][hapmap]
rs2039602	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039603	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039604	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221587	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2390014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656122	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs551219	1.00[CHB][hapmap]
rs55713534	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55912038	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57251624	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802232	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802233	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802235	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802236	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802237	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802238	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802244	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6420969	1.00[JPT][hapmap]
rs6576806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6663055	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663057	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675364	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675562	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678131	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690591	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6690902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67222626	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716178	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7550464	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7550559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550571	0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660356	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9660357	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12075854	COL24A1	cis	parietal	SCAN
rs12075854	LOC339524	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86577600-86580800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:86577800-86579000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:86577800-86579600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:86578400-86580600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:86578600-86585200	Weak transcription	Fetal Lung	lung

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