Variant report

Variant	rs9584576
Chromosome Location	chr13:98085156-98085157
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	SP1	chr13:98084895-98085896	GM12878	blood:	n/a	chr13:98085678-98085690 chr13:98085658-98085668 chr13:98085638-98085647 chr13:98085678-98085690 chr13:98085636-98085648 chr13:98085636-98085648 chr13:98085417-98085438 chr13:98085635-98085642 chr13:98085286-98085307
2	MAZ	chr13:98084721-98086670	GM12878	blood:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085403-98085414 chr13:98085402-98085415
3	MAFF	chr13:98085154-98085564	HepG2	liver:	n/a	n/a
4	HEY1	chr13:98084947-98086322	HepG2	liver:	n/a	n/a
5	MYC	chr13:98085152-98085160	MCF-7	breast:	n/a	n/a
6	RFX5	chr13:98084880-98086464	Hela-S3	cervix:	n/a	chr13:98085517-98085531 chr13:98085516-98085531
7	MXI1	chr13:98085152-98086202	Hela-S3	cervix:	n/a	n/a
8	E2F6	chr13:98084761-98086194	H1-hESC	embryonic stem cell:	n/a	chr13:98086090-98086101 chr13:98085297-98085306 chr13:98085384-98085393
9	POLR2A	chr13:98084686-98087246	GM19193	blood:	n/a	n/a
10	PAX5	chr13:98084989-98085764	GM12878	blood:	n/a	n/a
11	CREB1	chr13:98085042-98086007	ECC-1	luminal epithelium:	n/a	n/a
12	RCOR1	chr13:98084635-98086504	IMR90	lung:	n/a	n/a
13	E2F6	chr13:98084954-98085798	H1-hESC	embryonic stem cell:	n/a	chr13:98085297-98085306 chr13:98085384-98085393
14	POLR2A	chr13:98084527-98087335	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr13:98084760-98086269	SK-N-MC	brain:	n/a	n/a
16	MAFK	chr13:98084880-98086172	Hela-S3	cervix:	n/a	n/a
17	POU2F2	chr13:98084875-98085750	GM12891	blood:	n/a	n/a
18	RELA	chr13:98084570-98086193	GM19099	blood:	n/a	n/a
19	FOXP2	chr13:98085088-98085852	SK-N-MC	brain:	n/a	n/a
20	YY1	chr13:98084850-98085788	ECC-1	luminal epithelium:	n/a	n/a
21	MXI1	chr13:98084803-98087739	IMR90	lung:	n/a	n/a
22	MYBL2	chr13:98085000-98085895	HepG2	liver:	n/a	n/a
23	JUND	chr13:98085074-98085896	A549	lung:	n/a	chr13:98085565-98085579
24	CHD1	chr13:98084629-98085170	GM12878	blood:	n/a	n/a
25	POLR2A	chr13:98084848-98086280	GM12878	blood:	n/a	n/a
26	SRF	chr13:98085046-98085651	MCF-7	breast:	n/a	n/a
27	POLR2A	chr13:98084880-98086943	HL-60	blood:	n/a	n/a
28	POLR2A	chr13:98084910-98086318	ECC-1	luminal epithelium:	n/a	n/a
29	SP2	chr13:98085095-98085664	HepG2	liver:	n/a	chr13:98085636-98085645
30	ELF1	chr13:98084942-98085867	SK-N-SH	brain:	n/a	n/a
31	ZNF143	chr13:98085031-98086331	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr13:98084914-98087078	MCF-7	breast:	n/a	n/a
33	EP300	chr13:98085098-98085689	HepG2	liver:	n/a	n/a
34	POLR2A	chr13:98085028-98086290	HCT-116	colon:	n/a	n/a
35	BACH1	chr13:98085062-98085771	H1-hESC	embryonic stem cell:	n/a	n/a
36	IRF3	chr13:98084971-98085838	GM12878	blood:	n/a	chr13:98085678-98085692 chr13:98085636-98085650 chr13:98085384-98085393 chr13:98085297-98085306 chr13:98085657-98085671
37	POLR2A	chr13:98084907-98085877	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr13:98084510-98087400	GM19099	blood:	n/a	n/a
39	CREB1	chr13:98084926-98086607	HepG2	liver:	n/a	n/a
40	SP1	chr13:98084810-98086002	A549	lung:	n/a	chr13:98085678-98085690 chr13:98085658-98085668 chr13:98085984-98085993 chr13:98085638-98085647 chr13:98085678-98085690 chr13:98085636-98085648 chr13:98085636-98085648 chr13:98085417-98085438 chr13:98085635-98085642 chr13:98085286-98085307
41	MAX	chr13:98084913-98086034	A549	lung:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
42	USF1	chr13:98085128-98085705	A549	lung:	n/a	chr13:98085193-98085209
43	MAX	chr13:98084810-98085722	H1-hESC	embryonic stem cell:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
44	POLR2A	chr13:98084869-98086906	A549	lung:	n/a	n/a
45	POLR2A	chr13:98084594-98086327	SK-N-SH	brain:	n/a	n/a
46	MYC	chr13:98085018-98086381	MCF10A-Er-Src	breast:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
47	CHD1	chr13:98084569-98086399	IMR90	lung:	n/a	n/a
48	BRCA1	chr13:98085144-98086211	Hela-S3	cervix:	n/a	n/a
49	BHLHE40	chr13:98085153-98086201	HepG2	liver:	n/a	chr13:98085193-98085209
50	CREB1	chr13:98084992-98085906	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:98078675..98081221-chr13:98083499..98086151,3	MCF-7	breast:
2	chr13:98084839..98085346-chr3:186764394..186765071,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OXGR1-6	chr13:98081597-98086236	NONHSAT034832

Variant related genes	Relation type
RAP2A	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10161600	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161693	1.00[EUR][1000 genomes]
rs12100327	0.92[EUR][1000 genomes]
rs12184576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13378123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378459	0.92[EUR][1000 genomes]
rs13378494	0.83[AMR][1000 genomes]
rs13378500	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378554	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378832	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378938	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45560245	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55935003	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7318655	0.83[AMR][1000 genomes]
rs73564148	0.83[AMR][1000 genomes]
rs74105181	0.92[EUR][1000 genomes]
rs9300411	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9300414	0.82[EUR][1000 genomes]
rs9582131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9582132	0.83[AMR][1000 genomes]
rs9582133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9582134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9582136	0.83[AMR][1000 genomes]
rs9582144	0.83[AMR][1000 genomes]
rs9584567	0.92[EUR][1000 genomes]
rs9584570	0.92[EUR][1000 genomes]
rs9584572	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9584573	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9584574	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9584575	1.00[EUR][1000 genomes]
rs9584579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584582	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584583	1.00[AMR][1000 genomes]
rs9584595	0.83[AMR][1000 genomes]
rs9584596	0.83[AMR][1000 genomes]
rs9584599	0.83[AMR][1000 genomes]
rs9584615	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv1791802	chr13:98076911-98096882	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1804050	chr13:98076911-98096882	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1794802	chr13:98076911-98106042	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1797132	chr13:98076911-98106042	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562794	chr13:98083262-98086828	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv562795	chr13:98084675-98086470	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:98083200-98088000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr13:98083400-98088800	Active TSS	GM12878-XiMat	blood
3	chr13:98083600-98088200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr13:98083800-98088600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:98083800-98089200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr13:98084000-98088000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:98084000-98088600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr13:98084000-98088800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr13:98084000-98088800	Active TSS	Fetal Kidney	kidney
10	chr13:98084000-98089200	Active TSS	NHLF	lung
11	chr13:98084200-98085200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:98084200-98088000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:98084200-98088000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:98084200-98088000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:98084200-98088200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:98084200-98089000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:98084200-98089000	Active TSS	NHDF-Ad	bronchial
18	chr13:98084400-98085200	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr13:98084400-98085200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr13:98084400-98085200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:98084400-98085200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr13:98084400-98085200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr13:98084400-98085200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr13:98084400-98087200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr13:98084400-98087600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr13:98084400-98087600	Active TSS	A549	lung
27	chr13:98084400-98088000	Active TSS	Duodenum Mucosa	Duodenum
28	chr13:98084400-98088000	Active TSS	Rectal Smooth Muscle	rectum
29	chr13:98084400-98088200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:98084400-98088200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:98084400-98088400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:98084400-98088400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:98084400-98088400	Active TSS	Fetal Thymus	thymus
34	chr13:98084400-98088400	Active TSS	HSMM	muscle
35	chr13:98084400-98088600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr13:98084400-98088600	Active TSS	Fetal Muscle Leg	muscle
37	chr13:98084400-98088600	Active TSS	Fetal Stomach	stomach
38	chr13:98084400-98088800	Active TSS	H1 Cell Line	embryonic stem cell
39	chr13:98084400-98088800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:98084400-98088800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:98084400-98088800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:98084400-98089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:98084400-98089200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:98084400-98089200	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr13:98084400-98089600	Active TSS	Right Atrium	heart
46	chr13:98084600-98085200	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr13:98084600-98085200	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr13:98084600-98085200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr13:98084600-98085200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:98084600-98085200	Flanking Active TSS	Adipose Nuclei	Adipose

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