Variant report

Variant	rs7257060
Chromosome Location	chr19:39250800-39250801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11083478	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12972997	0.89[ASN][1000 genomes]
rs12977631	0.89[ASN][1000 genomes]
rs12985030	0.89[ASN][1000 genomes]
rs2086147	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2100941	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2368524	0.82[ASN][1000 genomes]
rs34054765	0.89[ASN][1000 genomes]
rs34090445	0.89[ASN][1000 genomes]
rs34305426	0.89[ASN][1000 genomes]
rs34361849	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34776027	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34834035	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35026669	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35253157	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35335944	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35502825	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35604174	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35974114	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4435378	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4473308	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4474812	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4491650	0.89[ASN][1000 genomes]
rs4801868	0.85[ASN][1000 genomes]
rs4802795	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802796	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56817884	0.89[ASN][1000 genomes]
rs58794115	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59073128	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61121905	0.89[ASN][1000 genomes]
rs61417362	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62120091	0.89[ASN][1000 genomes]
rs62120094	0.89[ASN][1000 genomes]
rs62120159	0.89[ASN][1000 genomes]
rs62121365	0.81[ASN][1000 genomes]
rs62121366	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62121373	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121374	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62121375	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253700	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7257063	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73554745	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508528	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8182597	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7257060	CAPN12	cis	multi-tissue	Pritchard
rs7257060	CAPN12	cis	Whole Blood	GTEx
rs7257060	CAPN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39246400-39270800	Weak transcription	K562	blood
2	chr19:39249000-39252200	Enhancers	HepG2	liver
3	chr19:39249000-39252800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:39249600-39250800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:39249800-39251400	Enhancers	Duodenum Mucosa	Duodenum
6	chr19:39249800-39251400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr19:39249800-39252400	Enhancers	Fetal Intestine Small	intestine
8	chr19:39250000-39250800	Enhancers	Spleen	Spleen
9	chr19:39250200-39253800	Enhancers	Fetal Intestine Large	intestine
10	chr19:39250400-39250800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39250400-39250800	Enhancers	Small Intestine	intestine
12	chr19:39250600-39250800	Enhancers	Liver	Liver
13	chr19:39250600-39253200	Weak transcription	A549	lung
14	chr19:39250800-39251800	Weak transcription	Liver	Liver

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