Variant report

Variant	rs58447742
Chromosome Location	chr13:76362682-76362683
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	POLR2A	chr13:76362655-76363332	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr13:76362616-76363232	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr13:76362440-76363088	SK-N-SH	brain:	n/a	n/a
4	FOS	chr13:76362654-76362992	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:76362616-76362967	HUVEC	blood vessel:	n/a	n/a
6	SIN3AK20	chr13:76362554-76362949	SK-N-SH	brain:	n/a	n/a
7	EP300	chr13:76362360-76363149	SK-N-SH	brain:	n/a	n/a
8	CHD2	chr13:76362640-76363217	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr13:76362667-76363375	Hela-S3	cervix:	n/a	n/a
10	FOSL2	chr13:76362475-76363102	SK-N-SH	brain:	n/a	n/a
11	MXI1	chr13:76362611-76363238	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr13:76362560-76363225	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr13:76362346-76363193	SK-N-SH	brain:	n/a	n/a
14	MAX	chr13:76362509-76362973	SK-N-SH	brain:	n/a	n/a
15	MYC	chr13:76362674-76362997	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr13:76362624-76362988	MCF10A-Er-Src	breast:	n/a	n/a
17	REST	chr13:76362636-76362934	SK-N-SH	brain:	n/a	n/a
18	FOS	chr13:76362652-76362931	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr13:76362470-76363065	SK-N-SH_RA	brain:	n/a	n/a
20	PBX3	chr13:76362425-76363129	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr13:76362447-76363136	HUVEC	blood vessel:	n/a	n/a
22	RCOR1	chr13:76362446-76363351	IMR90	lung:	n/a	n/a
23	POLR2A	chr13:76362474-76363126	SK-N-SH	brain:	n/a	n/a
24	TCF12	chr13:76362295-76363345	SK-N-SH	brain:	n/a	n/a
25	JUND	chr13:76362511-76363101	SK-N-SH	brain:	n/a	n/a
26	TAF1	chr13:76362681-76362943	SK-N-SH	brain:	n/a	n/a
27	RAD21	chr13:76362590-76362984	SK-N-SH_RA	brain:	n/a	chr13:76362937-76362950
28	POLR2A	chr13:76362603-76363351	Hela-S3	cervix:	n/a	n/a
29	TCF12	chr13:76362502-76363199	A549	lung:	n/a	n/a
30	FOS	chr13:76362625-76362994	MCF10A-Er-Src	breast:	n/a	n/a
31	TCF7L2	chr13:76362531-76363213	Hela-S3	cervix:	n/a	n/a
32	JUND	chr13:76362522-76363143	SK-N-SH	brain:	n/a	n/a
33	GATA2	chr13:76362612-76363311	HUVEC	blood vessel:	n/a	n/a
34	MAX	chr13:76362614-76363198	Hela-S3	cervix:	n/a	n/a
35	RXRA	chr13:76362436-76363218	SK-N-SH	brain:	n/a	n/a
36	USF1	chr13:76362643-76363134	SK-N-SH	brain:	n/a	n/a
37	TCF12	chr13:76362280-76363319	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr13:76362491-76363091	SK-N-SH	brain:	n/a	n/a
39	FOS	chr13:76362648-76362912	MCF10A-Er-Src	breast:	n/a	n/a
40	RXRA	chr13:76362550-76363136	SK-N-SH	brain:	n/a	n/a
41	EP300	chr13:76362474-76362981	SK-N-SH_RA	brain:	n/a	n/a
42	CEBPB	chr13:76362620-76363218	Hela-S3	cervix:	n/a	n/a
43	EP300	chr13:76362599-76363199	SK-N-SH	brain:	n/a	n/a
44	MAX	chr13:76362522-76362999	SK-N-SH	brain:	n/a	n/a
45	FOS	chr13:76362594-76363186	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr13:76362577-76362982	SK-N-SH	brain:	n/a	n/a
47	RFX5	chr13:76362637-76363180	Hela-S3	cervix:	n/a	n/a
48	GATA3	chr13:76362461-76363198	SK-N-SH	brain:	n/a	n/a
49	STAT3	chr13:76362675-76363054	MCF10A-Er-Src	breast:	n/a	chr13:76362953-76362965
50	TEAD4	chr13:76362426-76363122	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12428250	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12430034	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17065053	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17065074	0.83[ASN][1000 genomes]
rs1924094	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2120061	0.82[ASN][1000 genomes]
rs2241913	0.83[ASN][1000 genomes]
rs3759445	0.80[ASN][1000 genomes]
rs56030259	0.82[ASN][1000 genomes]
rs61958155	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61958156	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61958157	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61959560	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61959561	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9544047	0.82[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	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76338000-76362800	Weak transcription	Fetal Stomach	stomach
2	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
3	chr13:76340000-76363600	Weak transcription	Thymus	Thymus
4	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:76353400-76362800	Weak transcription	Lung	lung
7	chr13:76353400-76370600	Weak transcription	Primary T cells from cord blood	blood
8	chr13:76355600-76370800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr13:76357000-76362800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:76357000-76363000	Weak transcription	Fetal Kidney	kidney
11	chr13:76357000-76368400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:76357200-76363000	Weak transcription	Brain Anterior Caudate	brain
13	chr13:76357800-76362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:76357800-76363000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:76358200-76370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:76358200-76371400	Weak transcription	NHEK	skin
17	chr13:76358400-76362800	Weak transcription	Pancreas	Pancrea
18	chr13:76358400-76363000	Weak transcription	Psoas Muscle	Psoas
19	chr13:76358600-76362800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:76360200-76364000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:76360200-76367000	Genic enhancers	Osteobl	bone
22	chr13:76360800-76362800	Weak transcription	Right Ventricle	heart
23	chr13:76361000-76364400	Enhancers	NHLF	lung
24	chr13:76361200-76364200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr13:76361400-76362800	Enhancers	Fetal Intestine Small	intestine
26	chr13:76361400-76363000	Enhancers	Fetal Muscle Leg	muscle
27	chr13:76361400-76363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:76361400-76363200	Enhancers	HMEC	breast
29	chr13:76361400-76363400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:76361400-76363400	Enhancers	Ovary	ovary
31	chr13:76361400-76364000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:76361400-76364200	Enhancers	HepG2	liver
33	chr13:76361400-76364200	Enhancers	NH-A	brain
34	chr13:76361400-76364600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:76361400-76364600	Enhancers	Stomach Mucosa	stomach
36	chr13:76361400-76366400	Enhancers	Liver	Liver
37	chr13:76361600-76362800	Enhancers	HSMM	muscle
38	chr13:76361600-76363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:76361600-76363200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:76361600-76363800	Enhancers	Duodenum Mucosa	Duodenum
41	chr13:76361600-76364600	Enhancers	NHDF-Ad	bronchial
42	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:76361800-76363000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:76361800-76364200	Enhancers	Fetal Intestine Large	intestine
45	chr13:76361800-76377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:76362000-76362800	Weak transcription	Aorta	Aorta
47	chr13:76362000-76363000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr13:76362000-76363000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr13:76362000-76364200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr13:76362000-76366000	Enhancers	Fetal Heart	heart

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