Variant report

Variant	rs55780126
Chromosome Location	chr21:47238919-47238920
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47238547..47240191-chr21:47243403..47245083,2	K562	blood:
2	chr21:47237629..47240751-chr21:47286627..47289424,3	MCF-7	breast:
3	chr21:46973106..46978237-chr21:47237804..47242212,8	MCF-7	breast:
4	chr21:46961245..46963279-chr21:47238506..47240896,2	MCF-7	breast:
5	chr21:46976193..46978032-chr21:47237887..47240341,2	K562	blood:
6	chr21:47237289..47239387-chr21:47252638..47254672,2	K562	blood:
7	chr21:46871841..46874571-chr21:47238507..47240724,2	MCF-7	breast:
8	chr21:46973481..46977035-chr21:47238682..47244036,11	MCF-7	breast:
9	chr21:47230580..47232125-chr21:47237148..47240141,2	K562	blood:
10	chr21:47059881..47063838-chr21:47238507..47241456,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173638	Chromatin interaction
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1014446	0.83[ASN][1000 genomes]
rs10854472	0.87[ASN][1000 genomes]
rs11089024	0.87[ASN][1000 genomes]
rs12329841	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12329855	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12481867	0.87[ASN][1000 genomes]
rs12481913	0.85[ASN][1000 genomes]
rs12481970	0.86[ASN][1000 genomes]
rs12481977	0.87[ASN][1000 genomes]
rs12482010	0.86[ASN][1000 genomes]
rs12482094	0.87[ASN][1000 genomes]
rs12482377	0.87[ASN][1000 genomes]
rs12482405	0.86[EUR][1000 genomes]
rs12482648	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12482853	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351419	0.87[ASN][1000 genomes]
rs17351433	0.87[ASN][1000 genomes]
rs2065334	0.83[ASN][1000 genomes]
rs2094888	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2183595	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2183596	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838989	0.85[EUR][1000 genomes]
rs2838990	0.82[ASN][1000 genomes]
rs2838991	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838992	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838993	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838994	0.85[EUR][1000 genomes]
rs2838995	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838996	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838997	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838998	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838999	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839000	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839001	0.95[ASN][1000 genomes]
rs2839002	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839003	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839004	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839005	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839009	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2839013	0.87[ASN][1000 genomes]
rs2839014	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839026	0.87[ASN][1000 genomes]
rs2839029	0.83[ASN][1000 genomes]
rs2839032	0.83[ASN][1000 genomes]
rs28583990	0.85[EUR][1000 genomes]
rs3367	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35781238	0.91[ASN][1000 genomes]
rs3788208	0.83[ASN][1000 genomes]
rs3788209	0.87[ASN][1000 genomes]
rs3788211	0.87[ASN][1000 genomes]
rs3788215	0.85[ASN][1000 genomes]
rs3788216	0.87[ASN][1000 genomes]
rs3788220	0.87[ASN][1000 genomes]
rs3788224	0.83[ASN][1000 genomes]
rs3788227	0.87[ASN][1000 genomes]
rs4818798	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818801	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818802	0.87[ASN][1000 genomes]
rs4818803	0.87[ASN][1000 genomes]
rs4818805	0.83[ASN][1000 genomes]
rs4819151	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4819154	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4819155	0.87[ASN][1000 genomes]
rs4819156	0.87[ASN][1000 genomes]
rs4819157	0.87[ASN][1000 genomes]
rs55707606	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55856400	0.87[ASN][1000 genomes]
rs55875620	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55912352	0.87[ASN][1000 genomes]
rs55927540	0.90[ASN][1000 genomes]
rs56012600	0.84[EUR][1000 genomes]
rs56036552	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56256701	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56323347	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56347571	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56378934	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57688476	0.82[ASN][1000 genomes]
rs58952758	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59398815	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59785950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60604183	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61063225	0.85[ASN][1000 genomes]
rs61100346	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61276251	0.82[ASN][1000 genomes]
rs62211883	0.87[ASN][1000 genomes]
rs62211885	0.87[ASN][1000 genomes]
rs62211886	0.87[ASN][1000 genomes]
rs62211895	0.87[ASN][1000 genomes]
rs62211925	0.87[ASN][1000 genomes]
rs62211926	0.87[ASN][1000 genomes]
rs62213555	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214592	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214596	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214597	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214599	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62214604	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214608	0.83[ASN][1000 genomes]
rs66523344	0.87[ASN][1000 genomes]
rs66552772	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66991496	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67055992	0.87[ASN][1000 genomes]
rs67878041	0.87[ASN][1000 genomes]
rs72497640	0.84[AMR][1000 genomes]
rs7276632	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7280173	0.87[ASN][1000 genomes]
rs8127369	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8127428	0.87[ASN][1000 genomes]
rs8127809	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8128722	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs882668	0.81[ASN][1000 genomes]
rs882669	0.83[ASN][1000 genomes]
rs914241	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9637205	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9637206	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9637208	0.87[ASN][1000 genomes]
rs9647230	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs964975	0.87[ASN][1000 genomes]
rs9974491	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9977309	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977908	0.86[EUR][1000 genomes]
rs9978078	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9978740	0.85[EUR][1000 genomes]
rs9983770	0.87[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55780126	PCBP3	cis	Nerve Tibial	GTEx
rs55780126	PCBP3	cis	Muscle Skeletal	GTEx
rs55780126	PCBP3	cis	lung	GTEx
rs55780126	PCBP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47218000-47240200	Weak transcription	Pancreas	Pancrea
3	chr21:47221200-47239800	Weak transcription	Spleen	Spleen
4	chr21:47224000-47239000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:47236400-47243800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr21:47237200-47241200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr21:47237200-47241400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr21:47237400-47240200	Enhancers	HepG2	liver
9	chr21:47237400-47240400	Weak transcription	Fetal Kidney	kidney
10	chr21:47237400-47240600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr21:47237600-47240800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:47237800-47239000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr21:47238000-47240400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:47238000-47240600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr21:47238000-47240600	Enhancers	HMEC	breast
16	chr21:47238200-47239200	Enhancers	Osteobl	bone
17	chr21:47238200-47239400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr21:47238200-47239400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:47238200-47239600	Enhancers	NHEK	skin
20	chr21:47238200-47239800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:47238200-47239800	Enhancers	NHDF-Ad	bronchial
22	chr21:47238200-47240000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr21:47238200-47240600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr21:47238200-47240800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr21:47238200-47241000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:47238200-47241000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr21:47238200-47241000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr21:47238200-47241000	Enhancers	HSMM	muscle
29	chr21:47238400-47239000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr21:47238400-47239000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr21:47238400-47239000	Enhancers	Hela-S3	cervix
32	chr21:47238400-47241000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr21:47238400-47241000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr21:47238400-47241600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr21:47238600-47239000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr21:47238600-47239000	Flanking Active TSS	NH-A	brain
37	chr21:47238600-47239200	Enhancers	HSMMtube	muscle
38	chr21:47238600-47239400	Enhancers	Primary T cells from cord blood	blood
39	chr21:47238600-47239600	Enhancers	Thymus	Thymus
40	chr21:47238600-47240800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr21:47238600-47241000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr21:47238600-47241000	Enhancers	Fetal Muscle Leg	muscle
43	chr21:47238600-47241000	Enhancers	GM12878-XiMat	blood
44	chr21:47238800-47239000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr21:47238800-47239000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr21:47238800-47239000	Active TSS	A549	lung
47	chr21:47238800-47239200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr21:47238800-47239200	Weak transcription	Fetal Brain Female	brain
49	chr21:47238800-47239400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr21:47238800-47239400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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