Variant report

Variant	rs62121366
Chromosome Location	chr19:39244710-39244711
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11083478	0.85[AMR][1000 genomes]
rs2086147	0.83[AMR][1000 genomes]
rs2100941	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34361849	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34776027	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34834035	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35026669	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35253157	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35502825	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35604174	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35974114	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4435378	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4473308	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4474812	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802795	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802796	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58794115	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61417362	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62121364	0.90[ASN][1000 genomes]
rs62121373	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62121374	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62121375	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7257060	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7257063	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73554745	0.83[AMR][1000 genomes]
rs7508528	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[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	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62121366	CAPN12	cis	Whole Blood	GTEx
rs62121366	CAPN12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39236600-39245600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:39243600-39245000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39244200-39245200	Enhancers	K562	blood
4	chr19:39244400-39244800	Enhancers	HepG2	liver
5	chr19:39244400-39245000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:39244400-39245000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr19:39244400-39245000	Enhancers	Stomach Mucosa	stomach
8	chr19:39244600-39245800	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links