Variant report

Variant	rs56267013
Chromosome Location	chr4:20700298-20700299
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:20700057-20700382	A549	lung:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
2	GATA1	chr4:20700203-20700995	PBDE	blood:	n/a	n/a
3	CEBPB	chr4:20699992-20700456	MCF-7	breast:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
4	CEBPD	chr4:20699988-20700898	K562	blood:	n/a	chr4:20700219-20700230
5	CEBPB	chr4:20699967-20700805	K562	blood:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
6	TEAD4	chr4:20700113-20700855	K562	blood:	n/a	n/a
7	CTCF	chr4:20700280-20700430	HCM	heart:	n/a	n/a
8	MAX	chr4:20700010-20700379	NB4	blood:	n/a	n/a
9	CEBPB	chr4:20700054-20700411	IMR90	lung:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
10	NR2F2	chr4:20699985-20700953	K562	blood:	n/a	chr4:20700710-20700725
11	MYC	chr4:20700054-20700382	NB4	blood:	n/a	n/a
12	TAL1	chr4:20700095-20700916	K562	blood:	n/a	n/a
13	MYC	chr4:20700029-20700791	K562	blood:	n/a	n/a
14	CEBPB	chr4:20700053-20700351	H1-hESC	embryonic stem cell:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
15	ARID3A	chr4:20700015-20700842	K562	blood:	n/a	n/a
16	CEBPB	chr4:20700039-20700408	HepG2	liver:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
17	TEAD4	chr4:20700018-20700978	K562	blood:	n/a	n/a
18	JUN	chr4:20700155-20700842	K562	blood:	n/a	chr4:20700445-20700454
19	RCOR1	chr4:20700100-20700883	K562	blood:	n/a	n/a
20	CEBPB	chr4:20700088-20700367	K562	blood:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
21	MYC	chr4:20700132-20700322	H1-hESC	embryonic stem cell:	n/a	n/a
22	CEBPD	chr4:20699961-20700912	K562	blood:	n/a	chr4:20700219-20700230
23	JUND	chr4:20700105-20700809	K562	blood:	n/a	chr4:20700445-20700454
24	GATA1	chr4:20699846-20701050	K562	blood:	n/a	n/a
25	CEBPB	chr4:20700058-20700392	Hela-S3	cervix:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
26	RCOR1	chr4:20700092-20700835	K562	blood:	n/a	n/a
27	CEBPB	chr4:20699982-20700715	K562	blood:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
28	TBL1XR1	chr4:20699858-20700885	K562	blood:	n/a	n/a
29	MYC	chr4:20700012-20700865	K562	blood:	n/a	n/a
30	EP300	chr4:20700059-20700860	K562	blood:	n/a	chr4:20700219-20700233
31	CEBPB	chr4:20699983-20700439	MCF-7	breast:	n/a	chr4:20700220-20700231 chr4:20700218-20700229 chr4:20700218-20700231 chr4:20700218-20700231
32	CUX1	chr4:20699997-20700853	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:20700245..20702604-chr4:20707211..20709448,2	MCF-7	breast:
2	chr4:20699912..20701731-chr4:20714831..20716673,2	K562	blood:
3	chr4:20693086..20698959-chr4:20699230..20704175,9	K562	blood:

Variant related genes	Relation type
PACRGL	TF binding region
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10516361	1.00[ASN][1000 genomes]
rs1061836	0.81[ASN][1000 genomes]
rs1080125	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10805218	0.83[AMR][1000 genomes]
rs11721944	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11723855	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11733451	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11735866	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11736309	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11736477	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11737893	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12498799	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12503714	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509329	0.90[ASN][1000 genomes]
rs12510666	0.94[ASN][1000 genomes]
rs1365580	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1365581	0.96[ASN][1000 genomes]
rs1426882	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16869823	0.86[ASN][1000 genomes]
rs16869859	1.00[ASN][1000 genomes]
rs16869884	1.00[ASN][1000 genomes]
rs17552950	1.00[ASN][1000 genomes]
rs17622121	0.92[ASN][1000 genomes]
rs2291530	0.89[ASN][1000 genomes]
rs28439580	1.00[ASN][1000 genomes]
rs2874831	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57364495	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59020971	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs59687189	0.83[AMR][1000 genomes]
rs61790721	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61790747	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62410066	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62410087	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62410132	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62410133	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62410158	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62411661	0.92[ASN][1000 genomes]
rs6831523	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73101456	0.92[ASN][1000 genomes]
rs964020	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56267013	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs56267013	PACRGL	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20693400-20701200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:20700000-20701000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:20700000-20701000	Enhancers	Fetal Lung	lung
4	chr4:20700000-20701200	Enhancers	Osteobl	bone
5	chr4:20700200-20700400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:20700200-20700600	Flanking Active TSS	K562	blood
7	chr4:20700200-20701200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:20700200-20701200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr4:20700200-20701200	Weak transcription	Gastric	stomach
10	chr4:20700200-20701200	Weak transcription	Psoas Muscle	Psoas

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