Variant report

Variant	rs62107468
Chromosome Location	chr19:21489979-21489980
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11666447	0.82[EUR][1000 genomes]
rs11666525	0.82[EUR][1000 genomes]
rs11666540	0.87[EUR][1000 genomes]
rs11667103	0.89[EUR][1000 genomes]
rs11667361	0.87[EUR][1000 genomes]
rs11667392	0.83[EUR][1000 genomes]
rs11669033	0.82[EUR][1000 genomes]
rs11669790	0.87[EUR][1000 genomes]
rs11670815	0.87[EUR][1000 genomes]
rs11672341	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11672583	0.82[EUR][1000 genomes]
rs11673320	0.84[ASN][1000 genomes]
rs11879901	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1621154	0.89[EUR][1000 genomes]
rs1626404	0.89[EUR][1000 genomes]
rs1762578	0.89[EUR][1000 genomes]
rs17680605	0.82[EUR][1000 genomes]
rs1781867	0.89[EUR][1000 genomes]
rs1781872	0.89[EUR][1000 genomes]
rs2061916	0.87[EUR][1000 genomes]
rs2154302	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358993	0.82[EUR][1000 genomes]
rs2359145	0.82[EUR][1000 genomes]
rs279807	0.84[EUR][1000 genomes]
rs279809	0.85[EUR][1000 genomes]
rs4321312	0.87[EUR][1000 genomes]
rs4327181	0.84[EUR][1000 genomes]
rs4359573	0.87[EUR][1000 genomes]
rs4544364	0.87[EUR][1000 genomes]
rs55756795	0.87[EUR][1000 genomes]
rs55790393	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55875743	0.82[EUR][1000 genomes]
rs55899865	0.89[EUR][1000 genomes]
rs57299552	0.89[EUR][1000 genomes]
rs58412280	0.81[EUR][1000 genomes]
rs60173523	0.81[EUR][1000 genomes]
rs61035285	0.87[EUR][1000 genomes]
rs62107465	0.87[EUR][1000 genomes]
rs62107469	0.87[EUR][1000 genomes]
rs62107472	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107479	0.87[EUR][1000 genomes]
rs62107531	0.87[EUR][1000 genomes]
rs62107532	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107534	0.87[EUR][1000 genomes]
rs62107536	0.85[EUR][1000 genomes]
rs62107539	0.87[EUR][1000 genomes]
rs62107540	0.87[EUR][1000 genomes]
rs62107541	0.87[EUR][1000 genomes]
rs62109225	0.87[EUR][1000 genomes]
rs62109226	0.82[EUR][1000 genomes]
rs62109229	0.87[EUR][1000 genomes]
rs62110071	0.85[EUR][1000 genomes]
rs62110367	0.85[EUR][1000 genomes]
rs62110377	0.84[EUR][1000 genomes]
rs62110416	0.82[EUR][1000 genomes]
rs62110420	0.82[EUR][1000 genomes]
rs62110424	0.82[EUR][1000 genomes]
rs62110426	0.82[EUR][1000 genomes]
rs7246339	0.89[EUR][1000 genomes]
rs7251135	0.82[EUR][1000 genomes]
rs7258099	0.86[EUR][1000 genomes]
rs7258473	0.87[EUR][1000 genomes]
rs7258562	0.84[EUR][1000 genomes]
rs73537884	0.85[AFR][1000 genomes];0.87[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
rs62107468	ZNF708	cis	Thyroid	GTEx
rs62107468	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs62107468	ZNF708	cis	Muscle Skeletal	GTEx
rs62107468	RP11-678G14.2	cis	Whole Blood	GTEx
rs62107468	ZNF708	cis	lung	GTEx

Chromatin state (count:123 , 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	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
4	chr19:21474000-21490600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
7	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:21476000-21490400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:21476000-21490400	Weak transcription	Hela-S3	cervix
10	chr19:21476800-21497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:21477000-21494400	Weak transcription	Stomach Mucosa	stomach
12	chr19:21477200-21495000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:21477600-21495800	Weak transcription	HepG2	liver
14	chr19:21478000-21497400	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:21478200-21492600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:21478400-21500600	Weak transcription	Psoas Muscle	Psoas
17	chr19:21478600-21490600	Strong transcription	Fetal Lung	lung
18	chr19:21478600-21499200	Weak transcription	HMEC	breast
19	chr19:21480800-21490600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:21481000-21500600	Weak transcription	NHLF	lung
21	chr19:21481200-21493000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:21481600-21500000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:21481600-21500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:21481600-21505600	Weak transcription	K562	blood
25	chr19:21481800-21490600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr19:21481800-21492600	Strong transcription	Fetal Muscle Leg	muscle
27	chr19:21481800-21493000	Strong transcription	Dnd41	blood
28	chr19:21481800-21493400	Strong transcription	Fetal Stomach	stomach
29	chr19:21482000-21492400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:21482000-21493200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:21482000-21493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:21482200-21490400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:21482400-21492800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:21483000-21490000	Weak transcription	NHEK	skin
35	chr19:21483200-21492800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:21483400-21490600	Strong transcription	Ovary	ovary
37	chr19:21483600-21493000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr19:21483800-21490200	Strong transcription	HSMM	muscle
39	chr19:21484000-21490600	ZNF genes & repeats	GM12878-XiMat	blood
40	chr19:21484000-21492200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:21484200-21492200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:21484200-21494200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:21484400-21493200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:21484400-21511000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:21484600-21492400	Strong transcription	Fetal Intestine Large	intestine
46	chr19:21484800-21491400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:21484800-21492000	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:21485000-21493000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr19:21485200-21494000	Weak transcription	NHDF-Ad	bronchial
50	chr19:21485200-21495000	Weak transcription	Brain Inferior Temporal Lobe	brain

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