Variant report

Variant	rs12463354
Chromosome Location	chr19:21806111-21806112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10854054	0.88[ASN][1000 genomes]
rs11667151	0.88[ASN][1000 genomes]
rs11673280	0.95[ASN][1000 genomes]
rs11879044	0.81[ASN][1000 genomes]
rs11881160	0.94[ASN][1000 genomes]
rs11881176	0.94[ASN][1000 genomes]
rs11881813	0.94[ASN][1000 genomes]
rs12150968	0.95[ASN][1000 genomes]
rs12459011	0.95[ASN][1000 genomes]
rs12459715	0.90[ASN][1000 genomes]
rs12463384	0.95[ASN][1000 genomes]
rs12972148	0.81[ASN][1000 genomes]
rs12973209	0.90[ASN][1000 genomes]
rs12974817	0.81[ASN][1000 genomes]
rs12981277	0.88[ASN][1000 genomes]
rs1850937	0.90[ASN][1000 genomes]
rs2102920	0.81[ASN][1000 genomes]
rs2102922	0.90[ASN][1000 genomes]
rs2139530	0.90[ASN][1000 genomes]
rs2359157	0.90[ASN][1000 genomes]
rs34015922	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34835488	0.81[ASN][1000 genomes]
rs35092215	0.88[ASN][1000 genomes]
rs4435389	0.83[ASN][1000 genomes]
rs4809154	0.95[ASN][1000 genomes]
rs55851748	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57229007	0.88[ASN][1000 genomes]
rs57235280	0.90[ASN][1000 genomes]
rs59054166	0.81[ASN][1000 genomes]
rs59803919	0.95[ASN][1000 genomes]
rs61137407	0.88[ASN][1000 genomes]
rs61461318	0.95[ASN][1000 genomes]
rs62108370	0.94[ASN][1000 genomes]
rs62108372	0.96[ASN][1000 genomes]
rs62110244	0.81[ASN][1000 genomes]
rs62110249	0.88[ASN][1000 genomes]
rs6511273	0.89[ASN][1000 genomes]
rs6511275	0.97[ASN][1000 genomes]
rs71333832	0.95[ASN][1000 genomes]
rs7246154	0.90[ASN][1000 genomes]
rs7248367	0.90[ASN][1000 genomes]
rs7249639	0.94[ASN][1000 genomes]
rs7249775	0.95[ASN][1000 genomes]
rs7250960	0.88[ASN][1000 genomes]
rs7251076	0.95[ASN][1000 genomes]
rs7252080	0.92[ASN][1000 genomes]
rs7252081	0.92[ASN][1000 genomes]
rs7252104	0.92[ASN][1000 genomes]
rs7252205	0.95[ASN][1000 genomes]
rs7252706	0.95[ASN][1000 genomes]
rs7255395	0.95[ASN][1000 genomes]
rs7255521	0.94[ASN][1000 genomes]
rs7257246	0.90[ASN][1000 genomes]
rs7259763	0.95[ASN][1000 genomes]
rs7259888	0.95[ASN][1000 genomes]
rs7260016	0.80[ASN][1000 genomes]
rs7260175	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7260391	0.84[ASN][1000 genomes]
rs7260514	0.90[ASN][1000 genomes]
rs8100536	0.93[ASN][1000 genomes]
rs8101255	0.95[ASN][1000 genomes]
rs8101857	0.94[ASN][1000 genomes]
rs8110320	0.90[ASN][1000 genomes]
rs8111076	0.90[ASN][1000 genomes]
rs8112158	0.90[ASN][1000 genomes]
rs9749033	0.90[ASN][1000 genomes]
rs9749043	0.90[ASN][1000 genomes]
rs9749067	0.89[ASN][1000 genomes]
rs9749163	0.90[ASN][1000 genomes]
rs9749167	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv911423	chr19:21783995-21858994	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2760530	chr19:21798427-21885936	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv963135	chr19:21800743-21892052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12463354	RP11-678G14.2	cis	lung	GTEx
rs12463354	RP11-678G14.3	cis	lung	GTEx
rs12463354	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs12463354	ZNF429	cis	lung	GTEx
rs12463354	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs12463354	RP11-420K14.2	cis	Whole Blood	GTEx
rs12463354	ZNF100	cis	Muscle Skeletal	GTEx
rs12463354	RP11-678G14.3	cis	Thyroid	GTEx
rs12463354	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12463354	ZNF429	cis	Esophagus Mucosa	GTEx
rs12463354	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12463354	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs12463354	LOC400680	Cis_1M	lymphoblastoid	RTeQTL
rs12463354	RP11-420K14.2	cis	lung	GTEx
rs12463354	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs12463354	RP11-678G14.3	cis	Whole Blood	GTEx
rs12463354	ZNF429	cis	Whole Blood	GTEx
rs12463354	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12463354	ZNF208	cis	brain	BrainEAC

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21801400-21808000	Weak transcription	Dnd41	blood
2	chr19:21804800-21806200	ZNF genes & repeats	Fetal Intestine Small	intestine
3	chr19:21805000-21808800	Weak transcription	Fetal Intestine Large	intestine
4	chr19:21805400-21806600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21805600-21806800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
6	chr19:21805600-21806800	Enhancers	Brain Germinal Matrix	brain
7	chr19:21805800-21807800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr19:21806000-21807000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr19:21806000-21807200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr19:21806000-21807400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links