Variant report

Variant	rs55779022
Chromosome Location	chr3:54655363-54655364
allele	C/G
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	CTCF	chr3:54655320-54655470	SK-N-SH_RA	brain:	n/a	n/a
2	MXI1	chr3:54654759-54656033	SK-N-SH	brain:	n/a	n/a
3	EP300	chr3:54655292-54655560	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr3:54655126-54655735	SK-N-SH	brain:	n/a	chr3:54655383-54655393 chr3:54655374-54655391 chr3:54655383-54655392 chr3:54655253-54655263
5	POLR2A	chr3:54655115-54655612	U87	brain:	n/a	n/a
6	EP300	chr3:54655268-54655621	SK-N-SH_RA	brain:	n/a	n/a
7	REST	chr3:54655251-54655544	SK-N-SH	brain:	n/a	chr3:54655394-54655412 chr3:54655393-54655413
8	POLR2A	chr3:54655228-54655652	SK-N-MC	brain:	n/a	n/a
9	EP300	chr3:54654853-54656302	SK-N-SH	brain:	n/a	chr3:54655941-54655955 chr3:54656097-54656106 chr3:54655806-54655815 chr3:54655251-54655265
10	GATA2	chr3:54654941-54655846	SH-SY5Y	brain:	n/a	chr3:54655383-54655393 chr3:54655374-54655391 chr3:54655383-54655392 chr3:54655751-54655758 chr3:54655253-54655263
11	GATA1	chr3:54654859-54656252	PBDE	blood:	n/a	chr3:54656048-54656058 chr3:54656050-54656057 chr3:54655383-54655393 chr3:54655374-54655391 chr3:54655383-54655392 chr3:54656048-54656057 chr3:54655751-54655758 chr3:54655253-54655263
12	TCF12	chr3:54655139-54655762	SK-N-SH	brain:	n/a	n/a
13	FOXP2	chr3:54655247-54655552	SK-N-MC	brain:	n/a	n/a
14	TAL1	chr3:54655313-54655448	K562	blood:	n/a	chr3:54655374-54655392
15	CTCF	chr3:54655300-54655450	WERI-Rb-1	eye:	n/a	n/a
16	GATA3	chr3:54654885-54655736	SH-SY5Y	brain:	n/a	chr3:54655383-54655393 chr3:54655374-54655391 chr3:54655383-54655392 chr3:54655253-54655263

Variant related genes	Relation type
RPS15P5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10510769	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10510770	0.92[EUR][1000 genomes]
rs1130197	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17054227	0.92[EUR][1000 genomes]
rs17815617	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2359857	0.89[EUR][1000 genomes]
rs2884808	0.88[EUR][1000 genomes]
rs4345041	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4386460	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55772258	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56008232	0.89[EUR][1000 genomes]
rs56091855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56209938	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56260111	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56356828	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56976748	0.86[EUR][1000 genomes]
rs62255527	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62255532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255533	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62255534	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62255535	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62255536	0.84[AMR][1000 genomes]
rs62255538	0.82[EUR][1000 genomes]
rs6803005	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73068445	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55779022	ESRG	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54654400-54656400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:54654600-54655800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:54654600-54655800	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:54654800-54656200	Enhancers	HMEC	breast
8	chr3:54654800-54656200	Enhancers	HSMM	muscle
9	chr3:54654800-54662400	Weak transcription	Right Atrium	heart
10	chr3:54655000-54662400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:54655200-54655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:54655200-54656200	Enhancers	Brain Germinal Matrix	brain

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