Variant report

Variant	rs1542039
Chromosome Location	chr19:56984375-56984376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10408604	0.86[JPT][hapmap]
rs10416345	0.85[JPT][hapmap]
rs10419332	0.86[JPT][hapmap]
rs10421407	0.91[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs12973407	0.86[JPT][hapmap]
rs12981146	0.86[JPT][hapmap]
rs1542038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34163785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35461173	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35698251	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760849	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs3810340	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4281830	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4801163	0.91[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs917650	0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs917651	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs917652	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9304776	0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]

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	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1542039	ZNF329	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
6	chr19:56969400-56987600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:56972800-56987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:56975600-56985200	ZNF genes & repeats	Brain Germinal Matrix	brain
9	chr19:56975600-56987200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:56976800-56987200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:56978000-56984400	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:56979800-56985000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
13	chr19:56980000-56986000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr19:56980200-56985000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr19:56980400-56985800	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr19:56980400-56987200	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:56981000-56984800	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr19:56981000-56987600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:56981000-56988000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:56981200-56985200	ZNF genes & repeats	Aorta	Aorta
21	chr19:56981200-56985600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:56981400-56985400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:56981400-56986000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr19:56981400-56987600	ZNF genes & repeats	Ovary	ovary
25	chr19:56981600-56984400	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr19:56981600-56984400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr19:56981600-56984600	Strong transcription	Psoas Muscle	Psoas
28	chr19:56981600-56985200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:56982000-56984800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:56982000-56987600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:56982400-56984800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:56982600-56985400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:56982800-56986400	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr19:56983000-56988000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:56983200-56984400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:56983200-56987800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:56983400-56984800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:56983400-56984800	ZNF genes & repeats	Brain Angular Gyrus	brain
39	chr19:56983400-56984800	ZNF genes & repeats	Fetal Lung	lung
40	chr19:56983400-56985600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:56983600-56984800	ZNF genes & repeats	Fetal Kidney	kidney
42	chr19:56983600-56984800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
43	chr19:56983800-56984600	ZNF genes & repeats	Brain Hippocampus Middle	brain
44	chr19:56983800-56984600	Weak transcription	Dnd41	blood
45	chr19:56983800-56987600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:56983800-56987600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:56984000-56984400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:56984000-56984400	Weak transcription	Pancreas	Pancrea
49	chr19:56984000-56984800	Weak transcription	Fetal Stomach	stomach
50	chr19:56984000-56986400	Weak transcription	Brain Anterior Caudate	brain

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