Variant report

Variant	rs28898308
Chromosome Location	chr19:21696860-21696861
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11085456	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11666680	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668682	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11669130	0.81[ASN][1000 genomes]
rs12461802	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12609768	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12609823	0.81[ASN][1000 genomes]
rs12610154	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973084	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12974329	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975424	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12985995	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1401926	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879237	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879238	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2133822	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28498118	0.82[ASN][1000 genomes]
rs34040704	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34497957	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35782355	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3973190	0.81[ASN][1000 genomes]
rs4462731	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56346453	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511255	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511259	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247060	0.81[ASN][1000 genomes]
rs7250360	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250838	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251540	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7251620	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7251669	0.81[AMR][1000 genomes]
rs7252254	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253559	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7256389	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259317	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73017722	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101089	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101900	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106840	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109536	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8110814	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111885	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs924487	0.81[ASN][1000 genomes]
rs9789284	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	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
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs28898308	RP11-420K14.2	cis	Whole Blood	GTEx
rs28898308	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs28898308	RP11-678G14.2	cis	lung	GTEx
rs28898308	ZNF429	cis	Muscle Skeletal	GTEx
rs28898308	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28898308	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs28898308	RP11-678G14.2	cis	Thyroid	GTEx
rs28898308	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs28898308	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs28898308	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs28898308	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs28898308	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs28898308	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs28898308	ZNF100	cis	Muscle Skeletal	GTEx
rs28898308	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs28898308	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs28898308	CTD-2561J22.5	cis	Thyroid	GTEx
rs28898308	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28898308	CTD-2561J22.5	cis	lung	GTEx
rs28898308	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs28898308	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28898308	RP11-678G14.3	cis	Whole Blood	GTEx
rs28898308	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs28898308	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs28898308	RP11-678G14.3	cis	lung	GTEx
rs28898308	RP11-678G14.2	cis	Whole Blood	GTEx
rs28898308	ZNF429	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21689200-21702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21689200-21702000	Weak transcription	Stomach Mucosa	stomach
3	chr19:21689400-21698400	Weak transcription	Placenta	Placenta
4	chr19:21689400-21701200	Weak transcription	HSMMtube	muscle
5	chr19:21689400-21701600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:21689400-21701600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:21689400-21702000	Weak transcription	Left Ventricle	heart
8	chr19:21689400-21702000	Weak transcription	Right Ventricle	heart
9	chr19:21689600-21700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:21689600-21701400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:21689600-21701600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:21689600-21702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:21689800-21697800	Weak transcription	Psoas Muscle	Psoas
14	chr19:21690000-21701400	Weak transcription	Pancreas	Pancrea
15	chr19:21690000-21701600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:21690000-21701600	Weak transcription	Osteobl	bone
17	chr19:21690200-21698600	Weak transcription	Fetal Kidney	kidney
18	chr19:21690200-21701600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:21690200-21701600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:21690600-21699600	Weak transcription	Primary T cells from cord blood	blood
21	chr19:21690600-21701600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:21690600-21701600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:21691000-21698400	Weak transcription	Fetal Lung	lung
24	chr19:21691200-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:21691200-21702000	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:21691400-21697000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:21691400-21701200	Weak transcription	Fetal Heart	heart
28	chr19:21691400-21701600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:21691400-21702000	Weak transcription	Ovary	ovary
30	chr19:21691600-21699400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:21691600-21701000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:21692400-21701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:21693000-21698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:21694400-21697200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr19:21694600-21701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:21694800-21697000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:21695000-21697400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:21695000-21698000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr19:21695000-21700600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:21695000-21701400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:21695200-21700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:21695200-21701400	Weak transcription	Thymus	Thymus
43	chr19:21695200-21702000	Weak transcription	Spleen	Spleen
44	chr19:21695400-21697200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:21695400-21700800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:21695400-21701600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:21695800-21697200	Enhancers	Adipose Nuclei	Adipose
48	chr19:21695800-21698400	Weak transcription	Primary B cells from cord blood	blood
49	chr19:21696200-21697000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr19:21696200-21697000	Strong transcription	Brain Inferior Temporal Lobe	brain

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