Variant report

Variant	rs13115740
Chromosome Location	chr4:47465847-47465848
allele	A/C
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	chr4:47465192-47466028	IMR90	lung:	n/a	n/a
2	USF1	chr4:47465469-47465999	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr4:47465496-47466003	HepG2	liver:	n/a	n/a
4	EP300	chr4:47465599-47466130	GM12878	blood:	n/a	n/a
5	FOXP2	chr4:47465372-47465875	PFSK-1	brain:	n/a	n/a
6	MXI1	chr4:47465254-47466046	H1-hESC	embryonic stem cell:	n/a	chr4:47465735-47465744
7	SP1	chr4:47465259-47465892	H1-hESC	embryonic stem cell:	n/a	chr4:47465480-47465494 chr4:47465754-47465763 chr4:47465752-47465764 chr4:47465753-47465762 chr4:47465752-47465764 chr4:47465758-47465768
8	USF1	chr4:47465261-47466150	HCT-116	colon:	n/a	n/a
9	MAX	chr4:47465056-47466004	Hela-S3	cervix:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
10	ELF1	chr4:47465299-47465964	K562	blood:	n/a	chr4:47465653-47465666
11	POLR2A	chr4:47464732-47466112	GM19099	blood:	n/a	n/a
12	JUND	chr4:47465495-47466040	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:47465505-47465992	A549	lung:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
14	BRCA1	chr4:47465505-47465966	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:47465183-47465982	HCT-116	colon:	n/a	n/a
16	EP300	chr4:47465402-47465916	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr4:47465240-47465895	GM12878	blood:	n/a	n/a
18	USF1	chr4:47465292-47465943	HepG2	liver:	n/a	n/a
19	HEY1	chr4:47465244-47465863	HepG2	liver:	n/a	n/a
20	MAX	chr4:47465273-47466063	MCF-7	breast:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
21	YY1	chr4:47465422-47465851	ECC-1	luminal epithelium:	n/a	n/a
22	USF1	chr4:47465453-47466051	K562	blood:	n/a	n/a
23	BRCA1	chr4:47465421-47465876	Hela-S3	cervix:	n/a	n/a
24	FOS	chr4:47465601-47465914	MCF10A-Er-Src	breast:	n/a	n/a
25	USF1	chr4:47465272-47466068	SK-N-SH	brain:	n/a	n/a
26	TCF12	chr4:47465238-47465864	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr4:47465356-47466065	H1-hESC	embryonic stem cell:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
28	RCOR1	chr4:47465232-47465996	HepG2	liver:	n/a	n/a
29	MAX	chr4:47465339-47465988	H1-hESC	embryonic stem cell:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
30	E2F6	chr4:47464990-47465972	K562	blood:	n/a	chr4:47465785-47465794 chr4:47465565-47465575 chr4:47465748-47465757
31	POLR2A	chr4:47465284-47465964	HUVEC	blood vessel:	n/a	n/a
32	MXI1	chr4:47465229-47466041	GM12878	blood:	n/a	chr4:47465735-47465744
33	MTA3	chr4:47464887-47466011	GM12878	blood:	n/a	n/a
34	NRF1	chr4:47465588-47466124	K562	blood:	n/a	chr4:47465784-47465795 chr4:47465786-47465795 chr4:47465784-47465795 chr4:47465781-47465795 chr4:47465784-47465798
35	POLR2A	chr4:47465136-47465943	K562	blood:	n/a	n/a
36	SP4	chr4:47465355-47465915	H1-hESC	embryonic stem cell:	n/a	chr4:47465473-47465489
37	ATF3	chr4:47465456-47465941	HepG2	liver:	n/a	chr4:47465570-47465579
38	UBTF	chr4:47465252-47466029	K562	blood:	n/a	n/a
39	POLR2A	chr4:47465294-47465964	MCF-7	breast:	n/a	n/a
40	NRF1	chr4:47465286-47466009	GM12878	blood:	n/a	chr4:47465784-47465795 chr4:47465786-47465795 chr4:47465784-47465795 chr4:47465781-47465795 chr4:47465784-47465798
41	MAX	chr4:47465234-47466104	SK-N-SH	brain:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
42	USF1	chr4:47465235-47466048	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr4:47465130-47465913	GM12891	blood:	n/a	n/a
44	ZNF143	chr4:47465346-47465890	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr4:47465131-47466240	HCT-116	colon:	n/a	chr4:47465732-47465741 chr4:47465692-47465701 chr4:47465692-47465701 chr4:47465733-47465744 chr4:47465734-47465743
46	RFX5	chr4:47465488-47466012	GM12878	blood:	n/a	chr4:47465818-47465833
47	JUN	chr4:47465585-47465887	H1-hESC	embryonic stem cell:	n/a	n/a
48	NRF1	chr4:47465618-47465994	HepG2	liver:	n/a	chr4:47465784-47465795 chr4:47465786-47465795 chr4:47465784-47465795 chr4:47465781-47465795 chr4:47465784-47465798
49	BHLHE40	chr4:47465595-47465873	A549	lung:	n/a	n/a
50	POLR2A	chr4:47465120-47466063	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:47465818-47465868	GM12878	blood:	n/a
2	chr4:47465818-47465868	K562	blood:	n/a
3	chr4:47465818-47465868	HCM	heart:	n/a
4	chr4:47465818-47465868	SAEC	small airway:	n/a
5	chr4:47465818-47465868	HCT-116	colon:	n/a
6	chr4:47465818-47465868	HL-60	blood:	n/a
7	chr4:47465818-47465868	LNCaP	prostate:	n/a
8	chr4:47465818-47465868	T-47D	breast:	n/a
9	chr4:47465818-47465868	Hela-S3	cervix:	n/a
10	chr4:47465818-47465868	SK-N-SH	brain:	n/a
11	chr4:47465818-47465868	NH-A	brain:	n/a
12	chr4:47465818-47465868	HPAEpiC	pulmonary alveolar:	n/a
13	chr4:47465818-47465868	PrEC	prostate:	n/a
14	chr4:47465818-47465868	NB4	blood:	n/a
15	chr4:47465818-47465868	PANC-1	pancreas:	n/a
16	chr4:47465818-47465868	NT2-D1	testis:	n/a
17	chr4:47465818-47465868	ECC-1	luminal epithelium:	n/a
18	chr4:47465818-47465868	SK-N-SH_RA	brain:	n/a
19	chr4:47465818-47465868	HAEpiC	amniotic membrane:	n/a
20	chr4:47465818-47465868	MCF10A-Er-Src	breast:	n/a
21	chr4:47465818-47465868	HRE	kidney:	n/a
22	chr4:47465818-47465868	Jurkat	blood:	n/a
23	chr4:47465818-47465868	U87	brain:	n/a
24	chr4:47465818-47465868	HCF	heart:	n/a
25	chr4:47465818-47465868	BE2_C	brain:	n/a
26	chr4:47465818-47465868	IMR90	lung:	fetal
27	chr4:47465818-47465868	ovcar-3	ovarian:	n/a
28	chr4:47465818-47465868	HEEpiC	esophagus:	n/a
29	chr4:47465818-47465868	BJ	skin:	n/a
30	chr4:47465818-47465868	GM06990	blood:	n/a
31	chr4:47465818-47465868	Hepatocyte	liver:	n/a
32	chr4:47465818-47465868	NHBE	bronchial:	n/a
33	chr4:47465818-47465868	HNPCEpiC	eye:	n/a
34	chr4:47465818-47465868	AoSMC	blood vessel:	n/a
35	chr4:47465818-47465868	HIPEpiC	eye:	n/a
36	chr4:47465818-47465868	GM12891	blood:	n/a
37	chr4:47465818-47465868	HMEC	breast:	n/a
38	chr4:47465818-47465868	GM19239	blood:	n/a
39	chr4:47465818-47465868	AG10803	skin:	n/a
40	chr4:47465818-47465868	HEK293	kidney:	embryo
41	chr4:47465818-47465868	SKMC	muscle:	n/a
42	chr4:47465818-47465868	HRPEpiC	eye:	n/a
43	chr4:47465818-47465868	A549	lung:	n/a
44	chr4:47465818-47465868	ProgFib	skin:	n/a
45	chr4:47465818-47465868	GM12892	blood:	n/a
46	chr4:47465818-47465868	AG09319	gingival:	n/a
47	chr4:47465818-47465868	PFSK-1	brain:	n/a
48	chr4:47465818-47465868	AG04450	lung:	fetal
49	chr4:47465818-47465868	HUVEC	blood vessel:	n/a
50	chr4:47465818-47465868	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47465829..47468286-chr4:47470252..47472768,2	K562	blood:
2	chr4:47464764..47466968-chr8:67973543..67975836,2	MCF-7	breast:

Variant related genes	Relation type
COMMD8	TF binding region
COMMD8	CpG island
ENSG00000104218	Chromatin interaction
ENSG00000121022	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10938485	0.90[EUR][1000 genomes]
rs10938486	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11729677	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12645143	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13103660	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13129226	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140559	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16860200	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17600665	0.81[CEU][hapmap]
rs17653595	0.81[CEU][hapmap]
rs28409227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28436205	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28572263	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28588386	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589873	0.86[EUR][1000 genomes]
rs34022241	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096542	0.82[EUR][1000 genomes]
rs35143328	0.97[EUR][1000 genomes]
rs35197130	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35293354	0.86[EUR][1000 genomes]
rs35796318	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4070	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235149	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4235150	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4349580	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4435723	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4510445	0.96[EUR][1000 genomes]
rs4532215	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585276	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4694849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695233	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4695234	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59268722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447553	0.96[EUR][1000 genomes]
rs6447554	0.96[EUR][1000 genomes]
rs6843791	0.88[EUR][1000 genomes]
rs71611998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237075	1.00[ASN][1000 genomes]
rs73237093	1.00[ASN][1000 genomes]
rs73238618	1.00[ASN][1000 genomes]
rs73238622	1.00[ASN][1000 genomes]
rs7690580	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs9993271	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998984	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][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	nsv998919	chr4:47207023-47476876	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13115740	CORIN	cis	cerebellum	SCAN
rs13115740	GAP43	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47464400-47466000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:47464600-47466000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:47464600-47466000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:47464600-47466000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:47464600-47466000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:47464600-47466000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:47464600-47466000	Active TSS	Rectal Smooth Muscle	rectum
8	chr4:47464600-47466200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr4:47464600-47466200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:47464600-47466200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr4:47464600-47466200	Active TSS	NHLF	lung
12	chr4:47464600-47466400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:47464800-47466000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:47464800-47466000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:47464800-47466000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr4:47464800-47466000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:47464800-47466000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:47464800-47466000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:47464800-47466000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:47464800-47466000	Active TSS	Brain Anterior Caudate	brain
21	chr4:47464800-47466000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:47464800-47466200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:47464800-47466200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:47464800-47466200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:47464800-47466200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr4:47464800-47466200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:47464800-47466200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:47464800-47466200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:47464800-47466200	Active TSS	Colonic Mucosa	Colon
30	chr4:47464800-47466200	Active TSS	Fetal Muscle Trunk	muscle
31	chr4:47464800-47466200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr4:47464800-47466200	Active TSS	Right Atrium	heart
33	chr4:47464800-47466200	Active TSS	Right Ventricle	heart
34	chr4:47464800-47466200	Active TSS	Stomach Mucosa	stomach
35	chr4:47464800-47466200	Active TSS	A549	lung
36	chr4:47464800-47466200	Active TSS	HSMMtube	muscle
37	chr4:47464800-47466400	Active TSS	Fetal Brain Female	brain
38	chr4:47465000-47466000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr4:47465000-47466000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:47465000-47466000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:47465000-47466000	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr4:47465000-47466000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:47465000-47466000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:47465000-47466000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:47465000-47466000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:47465000-47466000	Active TSS	Brain Cingulate Gyrus	brain
47	chr4:47465000-47466000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr4:47465000-47466000	Active TSS	Esophagus	oesophagus
49	chr4:47465000-47466000	Active TSS	Fetal Intestine Large	intestine
50	chr4:47465000-47466000	Active TSS	Fetal Kidney	kidney

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