Variant report

Variant	rs2154302
Chromosome Location	chr19:21490411-21490412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10414834	0.85[EUR][1000 genomes]
rs10424079	0.81[EUR][1000 genomes]
rs11666213	0.85[EUR][1000 genomes]
rs11666447	0.89[EUR][1000 genomes]
rs11666525	0.89[EUR][1000 genomes]
rs11666540	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11667103	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11667361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11667392	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11669033	0.89[EUR][1000 genomes]
rs11669790	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11670815	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11670868	0.86[EUR][1000 genomes]
rs11672341	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11672583	0.91[EUR][1000 genomes]
rs11673320	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11879901	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13346641	0.81[EUR][1000 genomes]
rs1621154	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1626404	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1762578	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17680605	0.91[EUR][1000 genomes]
rs1781867	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1781872	0.98[EUR][1000 genomes]
rs2061916	0.96[EUR][1000 genomes]
rs2358993	0.91[EUR][1000 genomes]
rs2359144	0.81[EUR][1000 genomes]
rs2359145	0.89[EUR][1000 genomes]
rs2562405	0.81[EUR][1000 genomes]
rs2562413	0.81[EUR][1000 genomes]
rs2562416	0.84[EUR][1000 genomes]
rs2650776	0.84[EUR][1000 genomes]
rs2650844	0.81[EUR][1000 genomes]
rs2650848	0.81[EUR][1000 genomes]
rs279807	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs279809	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3853837	0.87[EUR][1000 genomes]
rs3853838	0.87[EUR][1000 genomes]
rs4321312	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4327181	0.93[EUR][1000 genomes]
rs4359573	0.96[EUR][1000 genomes]
rs4544364	0.96[EUR][1000 genomes]
rs4638726	0.84[EUR][1000 genomes]
rs55756795	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55790393	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55875743	0.91[EUR][1000 genomes]
rs55899865	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57299552	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58412280	0.91[EUR][1000 genomes]
rs60173523	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61035285	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62107465	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107468	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107469	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107472	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107479	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107531	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62107532	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107534	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62107536	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62107539	0.96[EUR][1000 genomes]
rs62107540	0.96[EUR][1000 genomes]
rs62107541	0.96[EUR][1000 genomes]
rs62109225	0.96[EUR][1000 genomes]
rs62109226	0.91[EUR][1000 genomes]
rs62109227	0.86[EUR][1000 genomes]
rs62109228	0.86[EUR][1000 genomes]
rs62109229	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62110071	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62110367	0.94[EUR][1000 genomes]
rs62110377	0.88[EUR][1000 genomes]
rs62110416	0.89[EUR][1000 genomes]
rs62110420	0.89[EUR][1000 genomes]
rs62110424	0.89[EUR][1000 genomes]
rs62110426	0.89[EUR][1000 genomes]
rs62110428	0.85[EUR][1000 genomes]
rs62110429	0.85[EUR][1000 genomes]
rs7246339	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7251135	0.89[EUR][1000 genomes]
rs7258099	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7258473	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7258562	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73537884	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	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
8	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2154302	RP11-678G14.2	cis	Whole Blood	GTEx
rs2154302	ZNF708	cis	Thyroid	GTEx
rs2154302	ZNF708	cis	lung	GTEx
rs2154302	ZNF708	cis	Muscle Skeletal	GTEx
rs2154302	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
3	chr19:21474000-21490600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
6	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:21476800-21497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:21477000-21494400	Weak transcription	Stomach Mucosa	stomach
9	chr19:21477200-21495000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:21477600-21495800	Weak transcription	HepG2	liver
11	chr19:21478000-21497400	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:21478200-21492600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:21478400-21500600	Weak transcription	Psoas Muscle	Psoas
14	chr19:21478600-21490600	Strong transcription	Fetal Lung	lung
15	chr19:21478600-21499200	Weak transcription	HMEC	breast
16	chr19:21480800-21490600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:21481000-21500600	Weak transcription	NHLF	lung
18	chr19:21481200-21493000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:21481600-21500000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:21481600-21500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:21481600-21505600	Weak transcription	K562	blood
22	chr19:21481800-21490600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr19:21481800-21492600	Strong transcription	Fetal Muscle Leg	muscle
24	chr19:21481800-21493000	Strong transcription	Dnd41	blood
25	chr19:21481800-21493400	Strong transcription	Fetal Stomach	stomach
26	chr19:21482000-21492400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:21482000-21493200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:21482000-21493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:21482400-21492800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:21483200-21492800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:21483400-21490600	Strong transcription	Ovary	ovary
32	chr19:21483600-21493000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:21484000-21490600	ZNF genes & repeats	GM12878-XiMat	blood
34	chr19:21484000-21492200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:21484200-21492200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:21484200-21494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:21484400-21493200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:21484600-21492400	Strong transcription	Fetal Intestine Large	intestine
40	chr19:21484800-21491400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:21484800-21492000	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:21485000-21493000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr19:21485200-21494000	Weak transcription	NHDF-Ad	bronchial
44	chr19:21485200-21495000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:21485400-21508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:21485400-21511200	Weak transcription	Gastric	stomach
47	chr19:21485600-21497600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:21485600-21504200	Weak transcription	Pancreas	Pancrea
49	chr19:21486200-21492000	Weak transcription	Colonic Mucosa	Colon
50	chr19:21486200-21493000	Strong transcription	Duodenum Mucosa	Duodenum

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