Variant report

Variant	rs62019432
Chromosome Location	chr15:43608680-43608681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43602565..43605136-chr15:43607378..43610157,2	K562	blood:
2	chr15:43608442..43611143-chr15:43626377..43627931,2	K562	blood:
3	chr15:43607344..43608879-chr15:43617306..43618965,2	MCF-7	breast:
4	chr15:43606779..43609028-chr15:43621318..43623726,3	MCF-7	breast:
5	chr15:43606648..43611125-chr15:43620820..43625585,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168803	Chromatin interaction
ENSG00000168806	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10518812	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12899865	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12900259	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905220	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12906017	0.83[AMR][1000 genomes]
rs12906481	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12907870	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12908460	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12911569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12911740	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12913977	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914122	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16957680	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957715	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16957730	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17723479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17780417	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17780920	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1814324	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2230451	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34002293	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34178146	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34181131	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34212866	0.81[EUR][1000 genomes]
rs34515241	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34591748	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633582	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34657657	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34661349	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34697113	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34715468	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34767197	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34860428	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34921640	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35158584	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35160541	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35278805	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35311230	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326382	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35681736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35903301	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35958032	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35975365	0.90[EUR][1000 genomes]
rs35992154	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36078097	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs514438	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55748552	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55801120	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60018990	0.83[AMR][1000 genomes]
rs62019442	0.81[EUR][1000 genomes]
rs62020574	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62020575	0.90[AMR][1000 genomes]
rs62021176	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021180	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66629206	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71476435	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7168220	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7173383	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7176923	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177146	0.83[AMR][1000 genomes]
rs7177892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7180812	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7181545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181634	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181783	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7182292	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7183708	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72707530	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72709850	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72709879	0.81[AMR][1000 genomes]
rs8027748	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62019432	TUBGCP4	cis	Artery Tibial	GTEx
rs62019432	ZSCAN29	cis	multi-tissue	Pritchard
rs62019432	TGM7	cis	Esophagus Mucosa	GTEx
rs62019432	LCMT2	cis	Esophagus Mucosa	GTEx
rs62019432	ZSCAN29	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43607600-43609200	Enhancers	Fetal Stomach	stomach
2	chr15:43607800-43609000	Enhancers	Stomach Smooth Muscle	stomach
3	chr15:43608200-43608800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:43608200-43608800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:43608200-43608800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:43608400-43608800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:43608400-43609400	Bivalent Enhancer	HepG2	liver
8	chr15:43608600-43609000	Enhancers	Fetal Lung	lung

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