Variant report

Variant	rs12407553
Chromosome Location	chr1:152297517-152297518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10788831	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888476	0.86[ASN][1000 genomes]
rs10888477	0.84[ASN][1000 genomes]
rs10888478	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204956	0.81[ASN][1000 genomes]
rs11204976	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204978	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11485508	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11576858	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11581433	0.81[EUR][1000 genomes]
rs11584340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584427	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11586114	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11588170	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12027807	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12027899	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12045492	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12045496	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12065368	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405241	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12405278	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12407156	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407748	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12407807	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12409802	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12730241	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858479	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1858480	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858482	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2050631	0.84[ASN][1000 genomes]
rs2065955	0.82[ASN][1000 genomes]
rs2065956	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2184950	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2184951	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2184953	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184954	0.81[EUR][1000 genomes]
rs2338555	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2338556	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3091276	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3120642	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3120653	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3120659	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3120661	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3120662	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126054	0.86[EUR][1000 genomes]
rs3126055	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3126056	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3126058	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126060	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126062	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3126066	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3126067	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3126072	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3126074	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3126079	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3126085	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126088	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126089	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126091	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3126092	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126094	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3126095	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126097	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3126098	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34188926	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41267154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4256811	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4341364	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4361987	0.80[ASN][1000 genomes]
rs4369233	0.82[AMR][1000 genomes]
rs4456097	0.82[ASN][1000 genomes]
rs4466659	0.83[ASN][1000 genomes]
rs4845753	0.84[ASN][1000 genomes]
rs55650366	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57672167	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58832908	0.82[AMR][1000 genomes]
rs6587666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6661167	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6681433	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66831674	0.91[EUR][1000 genomes]
rs6692010	0.81[ASN][1000 genomes]
rs71625201	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71625202	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72697000	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72698906	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74129461	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7540844	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543541	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9435974	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9436062	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][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	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv471348	chr1:152274651-152297679	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998298	chr1:152288685-152319877	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12407553	FLG	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152286600-152322200	Weak transcription	Ovary	ovary
2	chr1:152291800-152297800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152297200-152297600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152297200-152297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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