Variant report

Variant	rs57047253
Chromosome Location	chr5:68484609-68484610
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68484537-68486656	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr5:68484538-68485816	MCF10A-Er-Src	breast:	n/a	n/a
3	SIN3A	chr5:68484597-68486202	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBL1XR1	chr5:68484578-68486234	K562	blood:	n/a	n/a
5	MAX	chr5:68484567-68485886	SK-N-SH	brain:	n/a	n/a
6	SIN3AK20	chr5:68484602-68485951	SK-N-SH	brain:	n/a	n/a
7	YY1	chr5:68484593-68485915	SK-N-SH	brain:	n/a	n/a
8	MAX	chr5:68484553-68486236	A549	lung:	n/a	n/a
9	USF2	chr5:68484590-68485864	Hela-S3	cervix:	n/a	n/a
10	MYC	chr5:68484534-68486434	K562	blood:	n/a	n/a
11	POLR2A	chr5:68484592-68486144	K562	blood:	n/a	n/a
12	MXI1	chr5:68484490-68486399	IMR90	lung:	n/a	chr5:68485303-68485318 chr5:68485301-68485316
13	MXI1	chr5:68484372-68486482	SK-N-SH	brain:	n/a	chr5:68485303-68485318 chr5:68485301-68485316
14	CBX3	chr5:68484432-68485896	K562	blood:	n/a	n/a
15	POLR2A	chr5:68484536-68486346	PBDE	blood:	n/a	n/a
16	POLR2A	chr5:68484598-68486154	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:68484284-68486331	H1-hESC	embryonic stem cell:	n/a	n/a
18	SIN3AK20	chr5:68484381-68486009	MCF-7	breast:	n/a	n/a
19	GABPA	chr5:68484572-68486101	MCF-7	breast:	n/a	n/a
20	MAX	chr5:68484566-68485929	HepG2	liver:	n/a	n/a
21	GABPA	chr5:68484603-68485867	A549	lung:	n/a	n/a
22	POLR2A	chr5:68484552-68486487	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr5:68484591-68485908	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr5:68484548-68485890	MCF-7	breast:	n/a	n/a
25	POLR2A	chr5:68484489-68486449	HepG2	liver:	n/a	n/a
26	MAX	chr5:68484570-68485935	MCF-7	breast:	n/a	n/a
27	MXI1	chr5:68484484-68486299	K562	blood:	n/a	chr5:68485303-68485318 chr5:68485301-68485316
28	MAX	chr5:68484556-68485877	K562	blood:	n/a	n/a
29	RCOR1	chr5:68484577-68486097	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr5:68484543-68486243	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68484208..68487030-chr5:68662372..68666589,5	K562	blood:
2	chr5:68472735..68477267-chr5:68482092..68486946,8	MCF-7	breast:
3	chr5:68389777..68391751-chr5:68483907..68486743,2	MCF-7	breast:
4	chr5:68388464..68391397-chr5:68483791..68487195,4	K562	blood:
5	chr5:68388453..68391488-chr5:68483791..68487092,6	K562	blood:
6	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
7	chr5:68470678..68474023-chr5:68481300..68486180,5	MCF-7	breast:
8	chr5:68484557..68486514-chr5:68663480..68665519,2	MCF-7	breast:
9	chr5:68461460..68464018-chr5:68483608..68486992,6	MCF-7	breast:
10	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
11	chr5:68484254..68487485-chr5:68512131..68515372,4	K562	blood:
12	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC125-1	chr5:68483212-68485293	NONHSAT101896

No data

Variant related genes	Relation type
CENPH	TF binding region
ENSG00000152942	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515100	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940208	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188874	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271735	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271763	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271912	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846484	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56072942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176819	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58725071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59497209	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61699334	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67275234	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67693452	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867050	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72767837	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7709090	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714908	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734513	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57047253	CCDC125	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68471600-68484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:68484200-68484800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:68484200-68485000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:68484200-68485800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:68484200-68485800	Active TSS	Brain Germinal Matrix	brain
6	chr5:68484400-68484800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:68484400-68484800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:68484400-68484800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:68484400-68484800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr5:68484400-68484800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:68484400-68484800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr5:68484400-68484800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:68484400-68484800	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr5:68484400-68484800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr5:68484400-68484800	Flanking Active TSS	Fetal Lung	lung
16	chr5:68484400-68484800	Flanking Active TSS	Fetal Stomach	stomach
17	chr5:68484400-68484800	Flanking Active TSS	A549	lung
18	chr5:68484400-68484800	Flanking Active TSS	Osteobl	bone
19	chr5:68484400-68485000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr5:68484400-68485000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:68484400-68485000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:68484400-68485000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:68484400-68485000	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr5:68484400-68485000	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr5:68484400-68485000	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr5:68484400-68485000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr5:68484400-68485000	Flanking Active TSS	Hela-S3	cervix
28	chr5:68484400-68485000	Flanking Active TSS	HMEC	breast
29	chr5:68484400-68485000	Flanking Active TSS	HUVEC	blood vessel
30	chr5:68484400-68485200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:68484400-68485600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:68484400-68485600	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr5:68484400-68485600	Active TSS	HSMMtube	muscle
34	chr5:68484400-68485600	Active TSS	NH-A	brain
35	chr5:68484400-68485800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:68484400-68485800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr5:68484400-68485800	Active TSS	Fetal Brain Female	brain
38	chr5:68484400-68485800	Bivalent/Poised TSS	HepG2	liver
39	chr5:68484400-68485800	Active TSS	NHLF	lung
40	chr5:68484400-68486000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:68484400-68486000	Active TSS	NHEK	skin
42	chr5:68484400-68486200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:68484400-68486200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:68484400-68486200	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr5:68484400-68486200	Active TSS	Fetal Brain Male	brain
46	chr5:68484400-68486200	Active TSS	HSMM	muscle
47	chr5:68484400-68486200	Active TSS	NHDF-Ad	bronchial
48	chr5:68484400-68486400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr5:68484400-68486400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr5:68484400-68486400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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