Variant report

Variant	rs2059362
Chromosome Location	chr12:29396005-29396006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10450679	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10743651	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10743652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843365	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843372	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1120528	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12301475	0.83[AFR][1000 genomes]
rs1991113	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2194517	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2882294	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782507	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3782508	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4370971	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4412790	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6487789	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487791	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487792	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6487795	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487797	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487799	0.85[EUR][1000 genomes]
rs6487800	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487802	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487803	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7134187	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7137141	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295212	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7299648	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7299772	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7300032	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301575	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7302399	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303960	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73063614	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311081	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7316026	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766445	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954375	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954990	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7968167	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7968883	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7971296	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7972032	0.85[EUR][1000 genomes]
rs7974254	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976227	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7976667	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9669514	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9738165	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2059362	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29391600-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:29391800-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:29393200-29397000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:29393400-29396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:29394000-29396200	Enhancers	Colonic Mucosa	Colon
6	chr12:29394000-29396200	Enhancers	NHDF-Ad	bronchial
7	chr12:29394200-29396200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr12:29394200-29396200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:29394200-29396800	Enhancers	Stomach Mucosa	stomach
10	chr12:29394400-29396200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:29394400-29396400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:29394400-29397600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr12:29394400-29397800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:29394600-29396200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:29394600-29396200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:29394600-29396200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:29394600-29396200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:29394600-29396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:29394600-29396200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:29394600-29396200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:29394600-29396200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:29394600-29396200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:29394600-29396200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:29394600-29396200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr12:29394600-29396200	Enhancers	HMEC	breast
26	chr12:29394600-29396200	Enhancers	NH-A	brain
27	chr12:29394600-29396400	Enhancers	Liver	Liver
28	chr12:29394600-29396600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:29394600-29396600	Enhancers	Fetal Intestine Small	intestine
30	chr12:29394600-29396600	Enhancers	Fetal Kidney	kidney
31	chr12:29394600-29396800	Enhancers	Fetal Intestine Large	intestine
32	chr12:29394600-29396800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:29394600-29396800	Enhancers	GM12878-XiMat	blood
34	chr12:29394800-29396200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:29394800-29396200	Enhancers	Brain Anterior Caudate	brain
36	chr12:29394800-29396200	Enhancers	Brain Hippocampus Middle	brain
37	chr12:29394800-29396200	Enhancers	Colon Smooth Muscle	Colon
38	chr12:29394800-29396200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr12:29394800-29396200	Enhancers	Dnd41	blood
40	chr12:29394800-29396400	Enhancers	NHEK	skin
41	chr12:29395000-29396200	Enhancers	Osteobl	bone
42	chr12:29395000-29396600	Enhancers	Adipose Nuclei	Adipose
43	chr12:29395000-29397200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr12:29395000-29397400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr12:29395000-29397600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:29395000-29398800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:29395200-29396200	Enhancers	K562	blood
48	chr12:29395400-29396200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:29395400-29396800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:29395600-29396200	Enhancers	Fetal Thymus	thymus

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