Variant report

Variant	rs12483018
Chromosome Location	chr21:47064231-47064232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46961035..46963239-chr21:47061163..47064234,4	MCF-7	breast:
2	chr21:46963704..46966676-chr21:47062691..47065405,2	MCF-7	breast:
3	chr21:46960927..46963359-chr21:47063243..47066000,2	K562	blood:
4	chr21:47061926..47064777-chr21:47168199..47170677,2	MCF-7	breast:
5	chr21:47012314..47016239-chr21:47061189..47064828,5	K562	blood:

Variant related genes	Relation type
ENSG00000173638	Chromatin interaction
ENSG00000233922	Chromatin interaction
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1029014	0.85[EUR][1000 genomes]
rs12151963	0.83[EUR][1000 genomes]
rs12483701	0.83[EUR][1000 genomes]
rs1467758	0.90[EUR][1000 genomes]
rs17004799	0.83[EUR][1000 genomes]
rs1964928	0.85[EUR][1000 genomes]
rs1989537	0.88[EUR][1000 genomes]
rs2150460	0.85[EUR][1000 genomes]
rs2183601	0.90[EUR][1000 genomes]
rs2838973	0.89[EUR][1000 genomes]
rs2838974	0.89[EUR][1000 genomes]
rs2838976	0.89[EUR][1000 genomes]
rs2838978	0.82[EUR][1000 genomes]
rs2838981	0.85[EUR][1000 genomes]
rs2838982	0.84[EUR][1000 genomes]
rs2838983	0.83[EUR][1000 genomes]
rs2838985	0.84[EUR][1000 genomes]
rs2838988	0.82[EUR][1000 genomes]
rs28625750	0.82[EUR][1000 genomes]
rs3920695	0.87[EUR][1000 genomes]
rs4347938	0.89[EUR][1000 genomes]
rs4434082	0.89[EUR][1000 genomes]
rs4818795	0.86[EUR][1000 genomes]
rs4818797	0.82[EUR][1000 genomes]
rs4819134	0.82[EUR][1000 genomes]
rs4819144	0.83[EUR][1000 genomes]
rs55912508	0.81[EUR][1000 genomes]
rs55923134	0.86[EUR][1000 genomes]
rs55957843	0.85[EUR][1000 genomes]
rs56213918	0.91[EUR][1000 genomes]
rs56288252	0.91[EUR][1000 genomes]
rs57057834	0.87[EUR][1000 genomes]
rs57282159	0.86[EUR][1000 genomes]
rs57328058	0.83[EUR][1000 genomes]
rs57501220	0.89[EUR][1000 genomes]
rs57990579	0.90[EUR][1000 genomes]
rs58368336	0.82[EUR][1000 genomes]
rs58925015	0.85[EUR][1000 genomes]
rs60988006	0.85[EUR][1000 genomes]
rs61329313	0.86[EUR][1000 genomes]
rs61540945	0.82[EUR][1000 genomes]
rs62213277	0.82[EUR][1000 genomes]
rs62215031	0.89[EUR][1000 genomes]
rs62215035	0.89[EUR][1000 genomes]
rs62215040	0.88[EUR][1000 genomes]
rs62215047	0.85[EUR][1000 genomes]
rs62215048	0.85[EUR][1000 genomes]
rs62216072	0.82[EUR][1000 genomes]
rs62216073	0.80[EUR][1000 genomes]
rs67222545	0.83[EUR][1000 genomes]
rs67565220	0.90[EUR][1000 genomes]
rs725358	0.83[EUR][1000 genomes]
rs7279909	0.86[EUR][1000 genomes]
rs7280560	0.87[EUR][1000 genomes]
rs7283803	0.90[EUR][1000 genomes]
rs7410008	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs744506	0.84[EUR][1000 genomes]
rs767137	0.85[EUR][1000 genomes]
rs8133966	0.84[EUR][1000 genomes]
rs9306139	0.86[EUR][1000 genomes]
rs9637169	0.83[EUR][1000 genomes]
rs9647229	0.82[EUR][1000 genomes]
rs9976878	0.88[EUR][1000 genomes]
rs9978158	0.83[EUR][1000 genomes]
rs9978882	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9981586	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
5	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
6	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
7	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
8	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
10	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
11	nsv587864	chr21:47053453-47070718	Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
12	esv3338089	chr21:47061324-47064672	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv3448839	chr21:47061324-47065322	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	esv3376015	chr21:47061349-47064897	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv3326927	chr21:47061524-47065022	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12483018	PCBP3	cis	Nerve Tibial	GTEx
rs12483018	PCBP3	cis	lung	GTEx
rs12483018	PCBP3	cis	Muscle Skeletal	GTEx
rs12483018	PCBP3	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47062200-47064600	Active TSS	Colonic Mucosa	Colon
2	chr21:47062400-47064400	Active TSS	Ovary	ovary
3	chr21:47062400-47064400	Active TSS	Right Atrium	heart
4	chr21:47062400-47064600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr21:47062600-47064400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:47062600-47064400	Active TSS	Aorta	Aorta
7	chr21:47062600-47064600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr21:47062800-47064600	Active TSS	Right Ventricle	heart
9	chr21:47063200-47064400	Active TSS	Brain Germinal Matrix	brain
10	chr21:47063400-47064400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr21:47063600-47064400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr21:47063600-47064400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr21:47063600-47064400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr21:47063600-47064400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:47063600-47064400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr21:47063600-47064400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr21:47063600-47064400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr21:47063600-47064400	Active TSS	Primary T cells from cord blood	blood
19	chr21:47063600-47064400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr21:47063600-47064400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr21:47063600-47064400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:47063600-47064400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr21:47063600-47064400	Active TSS	Adipose Nuclei	Adipose
24	chr21:47063600-47064400	Active TSS	Brain Anterior Caudate	brain
25	chr21:47063600-47064400	Active TSS	Brain Hippocampus Middle	brain
26	chr21:47063600-47064400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:47063600-47064400	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
28	chr21:47063600-47064400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr21:47063600-47064400	Active TSS	Stomach Smooth Muscle	stomach
30	chr21:47063600-47064400	Active TSS	GM12878-XiMat	blood
31	chr21:47063600-47064400	Active TSS	HSMMtube	muscle
32	chr21:47063600-47064600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr21:47063600-47064600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:47063600-47064600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr21:47063600-47064600	Active TSS	Brain Angular Gyrus	brain
36	chr21:47063600-47064600	Active TSS	HSMM	muscle
37	chr21:47063600-47064600	Bivalent/Poised TSS	Osteobl	bone
38	chr21:47063600-47064800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr21:47063800-47064400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr21:47063800-47064400	Active TSS	Rectal Smooth Muscle	rectum
41	chr21:47063800-47064400	Bivalent/Poised TSS	NHLF	lung
42	chr21:47063800-47064600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr21:47063800-47064600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr21:47063800-47064600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr21:47064000-47064400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr21:47064000-47064400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr21:47064000-47064400	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr21:47064000-47064400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr21:47064000-47064400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr21:47064000-47064400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links