Variant report

Variant	rs12407807
Chromosome Location	chr1:152282311-152282312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10888483	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204976	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11204978	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204980	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204981	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11576858	0.84[AMR][1000 genomes]
rs11584340	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584427	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586114	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586631	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11588170	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12405241	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406105	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12407156	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12407553	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12407748	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730241	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1858479	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1858480	0.81[EUR][1000 genomes]
rs1858482	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2050631	0.96[ASN][1000 genomes]
rs2065955	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2065956	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184950	0.81[ASN][1000 genomes]
rs2184951	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2184953	0.82[ASN][1000 genomes]
rs2338555	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2338556	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3091276	0.80[EUR][1000 genomes]
rs3120659	0.81[EUR][1000 genomes]
rs3120662	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126058	0.80[ASN][1000 genomes]
rs3126060	0.80[ASN][1000 genomes]
rs3126062	0.81[ASN][1000 genomes]
rs3126066	0.95[EUR][1000 genomes]
rs3126067	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3126072	0.81[EUR][1000 genomes]
rs3126074	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3126079	0.82[ASN][1000 genomes]
rs3126085	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126088	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126089	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126092	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126094	0.81[EUR][1000 genomes]
rs3126095	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3126098	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34188926	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41267154	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4369233	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4582793	0.81[AMR][1000 genomes]
rs55650366	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55654502	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57672167	0.80[AMR][1000 genomes]
rs58832908	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587666	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661167	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681433	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681457	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6683653	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71625201	0.81[AMR][1000 genomes]
rs71625202	0.81[AMR][1000 genomes]
rs72697000	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72698906	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522925	0.84[EUR][1000 genomes]
rs9436062	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv18892	chr1:152274215-152287539	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	esv1810816	chr1:152274993-152286236	Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1827528	chr1:152274993-152286236	Strong transcription ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1812211	chr1:152275193-152286036	Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1826389	chr1:152275193-152286036	ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3394198	chr1:152279928-152282526	ZNF genes & repeats Weak transcription Strong transcription	CpG island	1 gene(s)	inside rSNPs	diseases
11	nsv824653	chr1:152280540-152283159	ZNF genes & repeats Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv159623	chr1:152280739-152284629	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12407807	FLG	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152274000-152283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:152277600-152282400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:152277600-152283600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:152278200-152288000	Weak transcription	Right Ventricle	heart
5	chr1:152279600-152283000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr1:152279600-152283400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:152279800-152284200	ZNF genes & repeats	Fetal Stomach	stomach
8	chr1:152280400-152286400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:152280600-152282600	ZNF genes & repeats	Aorta	Aorta
10	chr1:152280600-152283200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:152280600-152283800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:152280600-152284000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr1:152281200-152283000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
14	chr1:152281400-152283000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:152281600-152283000	ZNF genes & repeats	Ovary	ovary
16	chr1:152281600-152284800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:152282200-152284200	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr1:152282200-152284600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:152282200-152285000	ZNF genes & repeats	Brain Germinal Matrix	brain

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