Variant report

Variant	rs12153623
Chromosome Location	chr5:167437715-167437716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516039	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs11948431	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs11950941	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17069520	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17069547	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17069582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069617	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs17069662	1.00[JPT][hapmap]
rs2617958	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2617979	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs56117649	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56379512	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57271872	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58243181	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58485045	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66943039	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67727213	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6863895	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6882264	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72824974	0.96[ASN][1000 genomes]
rs73375658	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754925	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs889066	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9764066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830546	chr5:167303135-167456271	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12153623	FGF18	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167423400-167440600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:167423400-167455400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:167432400-167442400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:167432600-167442000	Weak transcription	NHEK	skin
5	chr5:167432800-167440800	Weak transcription	Fetal Brain Male	brain
6	chr5:167434000-167439000	Weak transcription	HSMM	muscle
7	chr5:167434200-167442200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:167434800-167447600	Weak transcription	NH-A	brain
9	chr5:167436400-167437800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:167437000-167441800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:167437200-167438200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:167437200-167438600	Weak transcription	Right Ventricle	heart
13	chr5:167437200-167438800	Enhancers	Fetal Lung	lung
14	chr5:167437200-167444000	Weak transcription	Left Ventricle	heart
15	chr5:167437400-167438800	Weak transcription	Fetal Heart	heart
16	chr5:167437600-167438000	Enhancers	Cortex derived primary cultured neurospheres	brain

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