Variant report

Variant	rs7252205
Chromosome Location	chr19:21797242-21797243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21784507..21786165-chr19:21795628..21798618,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10854054	0.93[ASN][1000 genomes]
rs11085469	0.83[ASN][1000 genomes]
rs11667151	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11673280	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879044	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11881160	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11881176	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11881813	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150968	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459011	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459715	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463354	0.95[ASN][1000 genomes]
rs12463384	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972148	0.86[ASN][1000 genomes]
rs12973203	0.83[ASN][1000 genomes]
rs12973209	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974817	0.86[ASN][1000 genomes]
rs12979255	0.83[ASN][1000 genomes]
rs12981277	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520068	0.83[ASN][1000 genomes]
rs1520069	0.83[ASN][1000 genomes]
rs1520070	0.83[ASN][1000 genomes]
rs1533674	0.82[ASN][1000 genomes]
rs1850937	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2102920	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2102922	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2139530	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359157	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34015922	0.97[ASN][1000 genomes]
rs34692125	0.83[ASN][1000 genomes]
rs34835488	0.86[ASN][1000 genomes]
rs35092215	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35229762	0.83[ASN][1000 genomes]
rs35465051	0.81[ASN][1000 genomes]
rs3817397	0.82[ASN][1000 genomes]
rs4435389	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4809151	0.83[ASN][1000 genomes]
rs4809152	0.83[ASN][1000 genomes]
rs4809154	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55851748	0.86[ASN][1000 genomes]
rs57229007	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57235280	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58083971	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59054166	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59803919	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61137407	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61461318	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108370	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62108372	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62110244	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62110249	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511273	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511275	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67854708	0.83[ASN][1000 genomes]
rs71333832	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248367	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249639	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7249775	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250457	0.83[ASN][1000 genomes]
rs7250470	0.83[ASN][1000 genomes]
rs7250663	0.83[ASN][1000 genomes]
rs7250960	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251111	0.83[ASN][1000 genomes]
rs7252080	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252081	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252104	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254018	0.83[ASN][1000 genomes]
rs7254378	0.83[ASN][1000 genomes]
rs7255081	0.83[ASN][1000 genomes]
rs7255395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255521	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256982	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7257246	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7259763	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259888	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260016	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7260175	0.92[ASN][1000 genomes]
rs7260391	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7260514	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8100536	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101255	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101857	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110320	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8111076	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8111313	0.82[ASN][1000 genomes]
rs8112158	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112960	0.81[ASN][1000 genomes]
rs9749033	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9749043	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9749067	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9749163	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9749167	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][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	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	nsv528643	chr19:21796943-21798441	Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7252205	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs7252205	ZNF429	cis	Whole Blood	GTEx
rs7252205	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7252205	ZNF429	cis	lung	GTEx
rs7252205	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs7252205	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs7252205	RP11-678G14.3	cis	lung	GTEx
rs7252205	RP11-678G14.3	cis	Whole Blood	GTEx
rs7252205	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7252205	LINC00664	cis	lung	GTEx
rs7252205	RP11-420K14.2	cis	lung	GTEx
rs7252205	LINC00664	cis	Whole Blood	GTEx
rs7252205	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs7252205	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7252205	ZNF429	cis	Esophagus Mucosa	GTEx
rs7252205	RP11-420K14.2	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21796000-21800600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:21796800-21800000	Weak transcription	Dnd41	blood
3	chr19:21797000-21797400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links