Variant report

Variant	rs12026971
Chromosome Location	chr1:56063733-56063734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10443236	0.82[CEU][hapmap];0.86[MEX][hapmap]
rs10493196	0.86[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10749702	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206625	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11206629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11206636	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11206637	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11206638	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11206639	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11206647	0.82[CEU][hapmap]
rs11206648	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs11206650	0.82[CEU][hapmap]
rs11807964	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12040862	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12041985	0.96[CEU][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12086546	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12117312	0.82[CEU][hapmap]
rs12124393	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs12132336	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12139752	0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12142554	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12401977	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12405865	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs1392128	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1392129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1392130	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1392131	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1392132	1.00[CEU][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1587432	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1604016	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17112402	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17417072	0.82[YRI][hapmap]
rs17417716	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17452876	0.85[CEU][hapmap]
rs56169646	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61776360	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61776375	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61776377	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6588566	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6669248	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6675850	0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7513395	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7525515	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7544458	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7546899	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7555929	0.96[CEU][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7556008	0.84[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12026971	C1orf168	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56056000-56066000	Weak transcription	Fetal Lung	lung
2	chr1:56059600-56076000	Weak transcription	Aorta	Aorta
3	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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