Variant report

Variant	rs1879238
Chromosome Location	chr19:21738753-21738754
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11085456	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666680	0.86[AMR][1000 genomes]
rs12461802	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610154	0.86[AMR][1000 genomes]
rs12973084	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12974329	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12985995	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1401926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133822	0.87[AMR][1000 genomes]
rs2562496	0.87[AFR][1000 genomes]
rs28898308	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34040704	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34497957	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35782355	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4462731	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4611587	0.91[AFR][1000 genomes]
rs6511255	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7250360	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251540	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251669	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7252254	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7253559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256389	0.82[AMR][1000 genomes]
rs7257186	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73017722	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8101089	0.86[AMR][1000 genomes]
rs8101900	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8106840	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110459	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8110814	0.80[ASN][1000 genomes]
rs8111885	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789284	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	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
9	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
10	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv543943	chr19:21713945-21759080	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv543944	chr19:21713945-21767567	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv543945	chr19:21717518-21767567	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs1879238	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs1879238	ZNF429	cis	Whole Blood	GTEx
rs1879238	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs1879238	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs1879238	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1879238	ZNF429	cis	Muscle Skeletal	GTEx
rs1879238	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1879238	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1879238	RP11-678G14.2	cis	Thyroid	GTEx
rs1879238	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs1879238	RP11-678G14.3	cis	lung	GTEx
rs1879238	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs1879238	RP11-678G14.2	cis	Whole Blood	GTEx
rs1879238	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs1879238	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs1879238	ZNF100	cis	Muscle Skeletal	GTEx
rs1879238	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs1879238	RP11-678G14.2	cis	lung	GTEx
rs1879238	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1879238	CTD-2561J22.5	cis	Thyroid	GTEx
rs1879238	RP11-420K14.2	cis	Whole Blood	GTEx
rs1879238	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs1879238	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs1879238	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs1879238	RP11-678G14.3	cis	Whole Blood	GTEx
rs1879238	CTD-2561J22.5	cis	lung	GTEx
rs1879238	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21720400-21740800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr19:21726400-21740800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:21726600-21740800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:21735800-21741600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:21735800-21744800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:21736200-21741400	ZNF genes & repeats	Liver	Liver
7	chr19:21736400-21743000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21737000-21738800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:21737200-21743000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:21737200-21747200	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr19:21737400-21738800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr19:21737400-21738800	ZNF genes & repeats	Fetal Intestine Large	intestine
13	chr19:21737400-21738800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
14	chr19:21737400-21739400	ZNF genes & repeats	Fetal Lung	lung
15	chr19:21737400-21739400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:21737400-21739600	ZNF genes & repeats	Fetal Stomach	stomach
17	chr19:21737600-21738800	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr19:21737600-21739000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:21737800-21738800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:21737800-21738800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:21737800-21738800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:21737800-21738800	ZNF genes & repeats	Aorta	Aorta
23	chr19:21737800-21738800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:21737800-21738800	ZNF genes & repeats	Thymus	Thymus
25	chr19:21737800-21739000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:21737800-21739800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:21738000-21738800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr19:21738000-21739000	Strong transcription	Dnd41	blood
29	chr19:21738000-21739400	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr19:21738000-21749400	Weak transcription	Left Ventricle	heart
31	chr19:21738000-21751400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr19:21738200-21738800	ZNF genes & repeats	Ovary	ovary
33	chr19:21738200-21739200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
34	chr19:21738200-21739400	Strong transcription	Brain Hippocampus Middle	brain
35	chr19:21738600-21740200	Weak transcription	Fetal Kidney	kidney
36	chr19:21738600-21740600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr19:21738600-21742400	Weak transcription	Right Ventricle	heart
38	chr19:21738600-21751600	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links