Variant report

Variant	rs9573566
Chromosome Location	chr13:76057043-76057044
allele	C/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	EP300	chr13:76055614-76057113	SK-N-SH	brain:	n/a	chr13:76055972-76055981 chr13:76056243-76056252 chr13:76056126-76056142 chr13:76056489-76056498 chr13:76056275-76056284 chr13:76056873-76056887
2	MXI1	chr13:76054261-76057449	SK-N-SH	brain:	n/a	chr13:76055275-76055284
3	POLR2A	chr13:76055939-76057047	U87	brain:	n/a	n/a
4	TBP	chr13:76056390-76057044	Hela-S3	cervix:	n/a	n/a
5	KAP1	chr13:76056349-76057046	HEK293	kidney:	n/a	n/a
6	ZBTB7A	chr13:76056395-76057078	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr13:76056342-76057101	GM12878	blood:	n/a	n/a
8	NFIC	chr13:76056320-76057111	GM12878	blood:	n/a	n/a
9	MAX	chr13:76054744-76057050	A549	lung:	n/a	chr13:76055278-76055294
10	CUX1	chr13:76056703-76057259	GM12878	blood:	n/a	chr13:76057229-76057243
11	RAD21	chr13:76056278-76057120	HCT-116	colon:	n/a	chr13:76056805-76056818 chr13:76056802-76056821
12	ZNF384	chr13:76056586-76057057	GM12878	blood:	n/a	n/a
13	BCLAF1	chr13:76056330-76057121	GM12878	blood:	n/a	chr13:76056410-76056423 chr13:76056352-76056361 chr13:76056873-76056882 chr13:76056407-76056420
14	RCOR1	chr13:76056575-76057049	GM12878	blood:	n/a	n/a
15	NFIC	chr13:76056401-76057117	GM12878	blood:	n/a	n/a
16	MTA3	chr13:76056576-76057093	GM12878	blood:	n/a	n/a
17	POLR2A	chr13:76054604-76057049	H1-hESC	embryonic stem cell:	n/a	n/a
18	SPI1	chr13:76056302-76057330	GM12878	blood:	n/a	chr13:76056873-76056882
19	RAD21	chr13:76056348-76057068	MCF-7	breast:	n/a	chr13:76056805-76056818 chr13:76056802-76056821
20	MEF2A	chr13:76056575-76057068	GM12878	blood:	n/a	chr13:76056875-76056883 chr13:76056845-76056860
21	GTF2F1	chr13:76056345-76057112	Hela-S3	cervix:	n/a	n/a
22	TBL1XR1	chr13:76056406-76057051	GM12878	blood:	n/a	n/a
23	RFX5	chr13:76056858-76057052	K562	blood:	n/a	n/a
24	POLR2A	chr13:76055864-76057079	PFSK-1	brain:	n/a	n/a
25	NFATC1	chr13:76056558-76057106	GM12878	blood:	n/a	n/a
26	MXI1	chr13:76054388-76057056	GM12878	blood:	n/a	chr13:76055275-76055284
27	CTCF	chr13:76056326-76057091	HCT-116	colon:	n/a	n/a
28	EP300	chr13:76056512-76057050	GM12878	blood:	n/a	chr13:76056873-76056887
29	PML	chr13:76055873-76057103	GM12878	blood:	n/a	n/a
30	MXI1	chr13:76054732-76057136	IMR90	lung:	n/a	chr13:76055275-76055284
31	MTA3	chr13:76056070-76057126	GM12878	blood:	n/a	n/a
32	MAZ	chr13:76055370-76057112	IMR90	lung:	n/a	n/a
33	CTCF	chr13:76056461-76057059	MCF-7	breast:	n/a	n/a
34	ATF2	chr13:76056368-76057096	GM12878	blood:	n/a	n/a
35	CHD1	chr13:76056496-76057074	GM12878	blood:	n/a	chr13:76056502-76056512
36	CTCF	chr13:76056327-76057258	HCT-116	colon:	n/a	n/a
37	RAD21	chr13:76054658-76057153	SK-N-SH	brain:	n/a	chr13:76056805-76056818 chr13:76055985-76055997 chr13:76056802-76056821
38	GATA3	chr13:76056220-76057119	SK-N-SH	brain:	n/a	chr13:76056359-76056366
39	MYC	chr13:76054820-76057069	MCF10A-Er-Src	breast:	n/a	chr13:76055278-76055294
40	CTCF	chr13:76055863-76057203	A549	lung:	n/a	n/a
41	FOXM1	chr13:76056259-76057148	GM12878	blood:	n/a	n/a
42	CTCF	chr13:76054716-76057196	SK-N-SH	brain:	n/a	chr13:76054882-76054890 chr13:76054881-76054889
43	MEF2C	chr13:76056511-76057079	GM12878	blood:	n/a	chr13:76056875-76056883 chr13:76056845-76056860

No.	Distal block	Cell Line	Cell type
1	chr13:75946564..75947349-chr13:76056407..76057240,4	MCF-7	breast:
2	chr13:76056260..76057375-chr13:76122984..76124053,8	MCF-7	breast:
3	chr13:76055919..76057695-chr13:76110507..76112437,2	MCF-7	breast:
4	chr13:76056486..76057156-chr16:7762589..7763109,2	MCF-7	breast:
5	chr13:76055248..76057886-chr13:76110224..76112780,4	MCF-7	breast:
6	chr13:76055434..76058277-chr13:76123047..76126766,3	K562	blood:

Variant related genes	Relation type
TBC1D4	TF binding region
ENSG00000188243	Chromatin interaction
ENSG00000261553	Chromatin interaction
ENSG00000118939	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1323691	0.82[ASN][1000 genomes]
rs1570539	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1570540	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1570541	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328945	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328946	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328947	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60343330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6562896	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7318786	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9318349	0.94[ASN][1000 genomes]
rs9543946	0.92[ASN][1000 genomes]
rs9543947	0.83[ASN][1000 genomes]
rs9565165	0.89[ASN][1000 genomes]
rs9565168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9565170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9573560	0.84[ASN][1000 genomes]
rs9573562	0.85[ASN][1000 genomes]
rs9573563	0.83[ASN][1000 genomes]
rs9573567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573571	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs961631	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv455987	chr13:75972846-76090084	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv562346	chr13:75972846-76090084	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76052000-76057400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr13:76053200-76057400	Active TSS	Fetal Kidney	kidney
3	chr13:76053400-76057200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr13:76053600-76057200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr13:76053600-76057400	Active TSS	Fetal Muscle Leg	muscle
6	chr13:76053600-76057400	Active TSS	NHDF-Ad	bronchial
7	chr13:76053800-76057200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr13:76053800-76057200	Active TSS	HSMMtube	muscle
9	chr13:76053800-76057400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:76054000-76057200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr13:76054000-76057400	Active TSS	HMEC	breast
12	chr13:76054000-76057400	Active TSS	NHLF	lung
13	chr13:76054200-76057200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:76054200-76057200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:76054200-76057400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:76054400-76057200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr13:76054400-76057200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:76054400-76057200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:76054400-76057200	Active TSS	Brain Anterior Caudate	brain
20	chr13:76054400-76057400	Active TSS	A549	lung
21	chr13:76054600-76057200	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr13:76054600-76057200	Active TSS	Placenta	Placenta
23	chr13:76054600-76057200	Active TSS	Osteobl	bone
24	chr13:76054800-76057200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr13:76054800-76057200	Active TSS	HSMM	muscle
26	chr13:76054800-76057400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:76055000-76057200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:76055000-76057200	Active TSS	Adipose Nuclei	Adipose
29	chr13:76055200-76057200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:76055200-76057200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:76055200-76057200	Active TSS	Brain Hippocampus Middle	brain
32	chr13:76055200-76057200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:76055200-76057200	Active TSS	Duodenum Mucosa	Duodenum
34	chr13:76055200-76057200	Active TSS	Fetal Intestine Large	intestine
35	chr13:76055200-76057200	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr13:76055200-76057200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr13:76055200-76057200	Active TSS	HUVEC	blood vessel
38	chr13:76055200-76057400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr13:76055200-76057600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:76055400-76057200	Active TSS	Fetal Stomach	stomach
41	chr13:76055600-76057200	Active TSS	H1 Cell Line	embryonic stem cell
42	chr13:76055600-76057200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:76055600-76057200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr13:76055600-76057200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr13:76055800-76057200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr13:76055800-76057200	Active TSS	Fetal Brain Female	brain
47	chr13:76055800-76057200	Active TSS	Stomach Smooth Muscle	stomach
48	chr13:76055800-76057400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr13:76055800-76057600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr13:76056000-76057200	Active TSS	Primary T cells from cord blood	blood

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