Variant report

Variant	rs1392130
Chromosome Location	chr1:56072554-56072555
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10443236	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs10493196	0.82[AMR][1000 genomes]
rs10749702	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11206625	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11206629	0.92[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11206636	1.00[ASW][hapmap];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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206638	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206639	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11206647	0.82[CEU][hapmap]
rs11206648	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs11206650	0.82[CEU][hapmap]
rs11807964	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12026971	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]
rs12040862	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12041985	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117312	0.82[CEU][hapmap]
rs12124393	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs12132336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139752	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142554	0.82[AMR][1000 genomes]
rs12405865	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs1392128	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1392129	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1392131	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1392132	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1587432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604016	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17112402	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs17417716	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17452876	0.85[CEU][hapmap];0.85[MKK][hapmap]
rs56169646	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61776360	0.81[AMR][1000 genomes]
rs61776375	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61776377	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6588566	0.86[EUR][1000 genomes]
rs6675850	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs709397	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7513395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525515	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7544458	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555929	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556008	0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769971	0.88[ASN][1000 genomes]
rs769984	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs1392130	C1orf168	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56059600-56076000	Weak transcription	Aorta	Aorta
2	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:56070200-56076200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:56070600-56076000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:56071200-56072800	Enhancers	Ovary	ovary
6	chr1:56071600-56076400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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