Variant report

Variant	rs12709959
Chromosome Location	chr19:56968314-56968315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11084447	0.82[ASN][1000 genomes]
rs11084448	0.90[ASN][1000 genomes]
rs12979827	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984960	0.90[ASN][1000 genomes]
rs17207432	0.86[AMR][1000 genomes]
rs17207481	0.86[AMR][1000 genomes]
rs2215410	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2288860	0.82[JPT][hapmap]
rs2288862	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288863	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28815239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35215648	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35520457	0.86[AMR][1000 genomes]
rs36147582	0.86[AMR][1000 genomes]
rs4239475	0.85[ASN][1000 genomes]
rs4801159	0.90[ASN][1000 genomes]
rs4801160	0.90[ASN][1000 genomes]
rs4801161	0.90[ASN][1000 genomes]
rs4801316	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4801318	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4801720	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs62121591	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62121592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121594	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121597	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6509995	0.82[ASN][1000 genomes]
rs7253851	0.90[ASN][1000 genomes]
rs8113270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs9646635	0.86[AMR][1000 genomes]
rs9749084	0.86[AMR][1000 genomes]
rs9749115	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12709959	ZNF582-AS1	cis	Artery Tibial	GTEx
rs12709959	ZNF324	cis	parietal	SCAN

Chromatin state (count:71 , 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	chr19:56957400-56974200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
3	chr19:56957400-56976800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
4	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:56960400-56968400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:56960600-56968600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:56960600-56969200	Weak transcription	Thymus	Thymus
10	chr19:56960600-56973800	Weak transcription	HSMM	muscle
11	chr19:56960800-56968400	Weak transcription	Pancreas	Pancrea
12	chr19:56961000-56968600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:56961600-56968600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:56963000-56968600	Weak transcription	Dnd41	blood
15	chr19:56963800-56970800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:56964400-56969000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:56964600-56970400	ZNF genes & repeats	Fetal Brain Female	brain
18	chr19:56964600-56971200	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr19:56964800-56970400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
20	chr19:56965000-56972400	Strong transcription	Brain Germinal Matrix	brain
21	chr19:56965200-56968600	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:56965400-56968400	Weak transcription	Fetal Thymus	thymus
23	chr19:56965800-56977400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:56966200-56970400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:56966400-56968400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:56966400-56968600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:56966400-56969200	ZNF genes & repeats	Psoas Muscle	Psoas
28	chr19:56966400-56970200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr19:56966400-56973000	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr19:56966400-56975200	ZNF genes & repeats	Liver	Liver
31	chr19:56966400-56979800	ZNF genes & repeats	Ovary	ovary
32	chr19:56966600-56968800	Weak transcription	Right Ventricle	heart
33	chr19:56966600-56973600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:56966800-56970600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:56967000-56968800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:56967000-56973200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:56967000-56973600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:56967000-56974000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:56967200-56968400	Weak transcription	Fetal Kidney	kidney
40	chr19:56967200-56968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:56967200-56971800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:56967200-56974000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
44	chr19:56967400-56969400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:56967400-56974200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:56967600-56968600	Strong transcription	Fetal Stomach	stomach
47	chr19:56967600-56969800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:56967600-56969800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
49	chr19:56967600-56969800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
50	chr19:56967600-56970000	Strong transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links