Variant report

Variant	rs12117758
Chromosome Location	chr1:56059054-56059055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1039294	0.84[CEU][hapmap]
rs10493193	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493194	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493195	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206626	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11206627	0.98[EUR][1000 genomes]
rs11206635	0.92[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206649	0.85[CEU][hapmap]
rs11801001	0.92[CEU][hapmap]
rs11805740	0.92[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116670	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12125730	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12139482	1.00[CEU][hapmap];0.89[MEX][hapmap]
rs17418048	0.85[CEU][hapmap]
rs17418151	0.85[CEU][hapmap]
rs17452287	0.85[CEU][hapmap]
rs1846562	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1846563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61566671	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6588567	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6670673	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6680818	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694680	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694786	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519540	0.85[CEU][hapmap]
rs7548272	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7549716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550575	0.85[CEU][hapmap]
rs769970	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs769989	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12117758	ZYG11A	cis	parietal	SCAN
rs12117758	DAB1	cis	parietal	SCAN
rs12117758	GLIS1	cis	cerebellum	SCAN
rs12117758	CPT2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56052800-56060400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56056000-56066000	Weak transcription	Fetal Lung	lung
3	chr1:56056200-56062400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:56057200-56059200	Enhancers	Right Atrium	heart
5	chr1:56058000-56059800	Enhancers	Fetal Stomach	stomach
6	chr1:56058600-56059400	Weak transcription	Aorta	Aorta
7	chr1:56058600-56060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:56059000-56059600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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