Variant report

Variant	rs62211925
Chromosome Location	chr21:47300840-47300841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46974485..46975268-chr21:47299866..47300947,3	MCF-7	breast:
2	chr21:47300298..47303074-chr21:47311902..47313864,2	K562	blood:
3	chr21:47240141..47240932-chr21:47300508..47301042,2	MCF-7	breast:
4	chr21:47298754..47301234-chr21:47302328..47305027,3	K562	blood:
5	chr21:47295466..47298745-chr21:47300328..47303080,5	MCF-7	breast:
6	chr21:47280227..47282087-chr21:47299384..47301576,2	MCF-7	breast:
7	chr21:47300028..47300909-chr21:47342650..47343811,5	MCF-7	breast:
8	chr21:47300119..47302715-chr21:47341992..47344397,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1014446	0.96[ASN][1000 genomes]
rs10854472	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089024	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481867	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12481970	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12481977	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482010	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12482094	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482377	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482853	0.87[ASN][1000 genomes]
rs17351419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351433	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065334	0.96[ASN][1000 genomes]
rs2838999	0.82[ASN][1000 genomes]
rs2839000	0.82[ASN][1000 genomes]
rs2839001	0.82[ASN][1000 genomes]
rs2839002	0.82[ASN][1000 genomes]
rs2839003	0.87[ASN][1000 genomes]
rs2839004	0.87[ASN][1000 genomes]
rs2839005	0.87[ASN][1000 genomes]
rs2839009	0.84[ASN][1000 genomes]
rs2839013	0.93[ASN][1000 genomes]
rs2839014	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839026	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839029	0.96[ASN][1000 genomes]
rs2839032	0.96[ASN][1000 genomes]
rs3788208	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788209	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788211	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788215	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788216	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788220	1.00[ASN][1000 genomes]
rs3788224	0.96[ASN][1000 genomes]
rs3788227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818801	0.82[ASN][1000 genomes]
rs4818802	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818803	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818805	0.96[ASN][1000 genomes]
rs4819151	0.82[ASN][1000 genomes]
rs4819152	0.82[ASN][1000 genomes]
rs4819154	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819155	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819156	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819157	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780126	0.87[ASN][1000 genomes]
rs55856400	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875620	0.87[ASN][1000 genomes]
rs55912352	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55927540	0.96[ASN][1000 genomes]
rs55996718	0.81[EUR][1000 genomes]
rs56256701	0.81[ASN][1000 genomes]
rs57688476	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58952758	0.82[ASN][1000 genomes]
rs59785950	0.82[ASN][1000 genomes]
rs61063225	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61276251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62211883	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211885	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211886	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211894	0.84[AFR][1000 genomes]
rs62211895	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214592	0.82[ASN][1000 genomes]
rs62214596	0.82[ASN][1000 genomes]
rs62214597	0.82[ASN][1000 genomes]
rs62214599	0.82[ASN][1000 genomes]
rs62214604	0.87[ASN][1000 genomes]
rs62214608	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66523344	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66991496	0.82[ASN][1000 genomes]
rs67055992	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67878041	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280173	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127428	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882668	0.94[ASN][1000 genomes]
rs882669	0.96[ASN][1000 genomes]
rs9637208	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964975	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983770	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	esv14817	chr21:47293464-47303825	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
22	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62211925	PCBP3	cis	Muscle Skeletal	GTEx
rs62211925	PCBP3	cis	lung	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47295600-47309200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:47298000-47306600	Weak transcription	NH-A	brain
3	chr21:47299200-47301800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr21:47299400-47301600	Enhancers	Primary T cells from cord blood	blood
5	chr21:47299600-47301400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr21:47299600-47301600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr21:47299600-47302000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr21:47299600-47302600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr21:47299600-47303000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr21:47299800-47301000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr21:47299800-47301000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr21:47299800-47301000	Enhancers	Brain Hippocampus Middle	brain
13	chr21:47299800-47301000	Enhancers	Brain Substantia Nigra	brain
14	chr21:47299800-47301000	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr21:47299800-47301200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr21:47299800-47301200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr21:47299800-47301200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr21:47299800-47301200	Enhancers	HSMM	muscle
19	chr21:47299800-47301600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr21:47299800-47301600	Enhancers	Fetal Thymus	thymus
21	chr21:47299800-47302000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr21:47300000-47301000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:47300000-47301000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:47300000-47301000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr21:47300000-47301000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr21:47300000-47301000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr21:47300000-47301000	Enhancers	Adipose Nuclei	Adipose
28	chr21:47300000-47301000	Enhancers	Brain Anterior Caudate	brain
29	chr21:47300000-47301000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr21:47300000-47301000	Enhancers	Spleen	Spleen
31	chr21:47300000-47301000	Enhancers	HSMMtube	muscle
32	chr21:47300000-47301000	Enhancers	NHDF-Ad	bronchial
33	chr21:47300000-47301200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr21:47300000-47301400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr21:47300000-47302200	Enhancers	Brain Cingulate Gyrus	brain
36	chr21:47300200-47301000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr21:47300200-47301000	Enhancers	Esophagus	oesophagus
38	chr21:47300200-47301000	Enhancers	Thymus	Thymus
39	chr21:47300200-47301200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr21:47300200-47301200	Flanking Active TSS	NHEK	skin
41	chr21:47300200-47301600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr21:47300400-47301000	Flanking Active TSS	HMEC	breast
43	chr21:47300400-47305400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr21:47300400-47305800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr21:47300600-47301000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr21:47300600-47301000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr21:47300600-47301000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr21:47300600-47301200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr21:47300600-47306000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr21:47300800-47301000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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