Variant report

Variant	rs3750259
Chromosome Location	chr8:49647910-49647911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr8:49647620-49648490	H1-hESC	embryonic stem cell:	n/a	chr8:49647791-49647800 chr8:49648232-49648240
2	E2F6	chr8:49647674-49648576	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr8:49647689-49648052	H1-hESC	embryonic stem cell:	n/a	chr8:49647856-49647871 chr8:49647854-49647869
4	CTCF	chr8:49647880-49648030	AoAF	blood vessel:	n/a	n/a
5	RAD21	chr8:49647645-49648142	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr8:49647900-49648050	HA-sp	spinal cord:	n/a	n/a
7	MAX	chr8:49647589-49648368	A549	lung:	n/a	chr8:49647860-49647869
8	E2F6	chr8:49647271-49648512	H1-hESC	embryonic stem cell:	n/a	chr8:49647555-49647567
9	POLR2A	chr8:49647735-49648052	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr8:49647880-49648030	BJ	skin:	n/a	n/a
11	CTCF	chr8:49647860-49648010	HPF	lung:	n/a	n/a
12	MAX	chr8:49647384-49648345	H1-hESC	embryonic stem cell:	n/a	chr8:49647860-49647869
13	CTCF	chr8:49647900-49648050	NHEK	skin:	n/a	n/a
14	MAX	chr8:49647457-49648374	H1-hESC	embryonic stem cell:	n/a	chr8:49647860-49647869
15	CTCF	chr8:49647880-49648030	HCM	heart:	n/a	n/a
16	CHD2	chr8:49647594-49648243	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr8:49647686-49648064	A549	lung:	n/a	n/a
18	CTCF	chr8:49647900-49648050	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr8:49647900-49648050	HCPEpiC	choroid plexus:	n/a	n/a
20	CTCF	chr8:49647900-49648050	HRPEpiC	eye:	n/a	n/a
21	CTCF	chr8:49647900-49648050	HPF	lung:	n/a	n/a
22	CTCF	chr8:49647880-49648030	HVMF	connective:	n/a	n/a
23	CTCF	chr8:49647860-49648010	HPAF	blood vessel:	n/a	n/a
24	CTCF	chr8:49647760-49647910	A549	lung:	n/a	n/a
25	CTCF	chr8:49647900-49648050	HUVEC	blood vessel:	n/a	n/a
26	JUND	chr8:49647775-49647923	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr8:49647820-49647970	NHDF-neo	bronchial:	n/a	n/a
28	ZNF143	chr8:49647773-49648097	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F4	chr8:49647768-49648002	MCF10A-Er-Src	breast:	n/a	n/a
30	CTCF	chr8:49647880-49648030	SAEC	small airway:	n/a	n/a
31	BRCA1	chr8:49647689-49648150	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr8:49647698-49648531	H1-hESC	embryonic stem cell:	n/a	chr8:49647860-49647869
33	RAD21	chr8:49647701-49648491	H1-hESC	embryonic stem cell:	n/a	n/a
34	GTF2F1	chr8:49647756-49648081	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr8:49647860-49648010	HVMF	connective:	n/a	n/a
36	CTCF	chr8:49647880-49648030	HMF	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:49647907-49647957	HepG2	liver:	n/a
2	chr8:49647907-49647957	GM12892	blood:	n/a
3	chr8:49647907-49647957	HL-60	blood:	n/a
4	chr8:49647907-49647957	U87	brain:	n/a
5	chr8:49647907-49647957	BE2_C	brain:	n/a
6	chr8:49647907-49647957	LNCaP	prostate:	n/a
7	chr8:49647907-49647957	HUVEC	blood vessel:	n/a
8	chr8:49647907-49647957	AG09319	gingival:	n/a
9	chr8:49647907-49647957	NHDF-neo	bronchial:	n/a
10	chr8:49647907-49647957	CMK	blood:	n/a
11	chr8:49647907-49647957	SK-N-SH	brain:	n/a
12	chr8:49647907-49647957	PANC-1	pancreas:	n/a
13	chr8:49647907-49647957	HMEC	breast:	n/a
14	chr8:49647907-49647957	T-47D	breast:	n/a
15	chr8:49647907-49647957	HIPEpiC	eye:	n/a
16	chr8:49647907-49647957	GM12878	blood:	n/a
17	chr8:49647907-49647957	HRE	kidney:	n/a
18	chr8:49647907-49647957	IMR90	lung:	fetal
19	chr8:49647907-49647957	SAEC	small airway:	n/a
20	chr8:49647907-49647957	H1-hESC	embryonic stem cell:	embryo
21	chr8:49647907-49647957	GM06990	blood:	n/a
22	chr8:49647907-49647957	HCF	heart:	n/a
23	chr8:49647907-49647957	PrEC	prostate:	n/a
24	chr8:49647907-49647957	HRPEpiC	eye:	n/a
25	chr8:49647907-49647957	HPAEpiC	pulmonary alveolar:	n/a
26	chr8:49647907-49647957	AG04450	lung:	fetal
27	chr8:49647907-49647957	AoSMC	blood vessel:	n/a
28	chr8:49647907-49647957	Hela-S3	cervix:	n/a
29	chr8:49647907-49647957	SK-N-SH_RA	brain:	n/a
30	chr8:49647907-49647957	NHBE	bronchial:	n/a
31	chr8:49647907-49647957	SK-N-MC	brain:	n/a
32	chr8:49647907-49647957	A549	lung:	n/a
33	chr8:49647907-49647957	Caco-2	colon:	n/a
34	chr8:49647907-49647957	BJ	skin:	n/a
35	chr8:49647907-49647957	K562	blood:	n/a
36	chr8:49647907-49647957	HAEpiC	amniotic membrane:	n/a
37	chr8:49647907-49647957	ECC-1	luminal epithelium:	n/a
38	chr8:49647907-49647957	MCF-7	breast:	n/a
39	chr8:49647907-49647957	ovcar-3	ovarian:	n/a
40	chr8:49647907-49647957	HCM	heart:	n/a
41	chr8:49647907-49647957	HCT-116	colon:	n/a
42	chr8:49647907-49647957	HEK293	kidney:	embryo
43	chr8:49647907-49647957	Jurkat	blood:	n/a
44	chr8:49647907-49647957	ProgFib	skin:	n/a
45	chr8:49647907-49647957	PFSK-1	brain:	n/a
46	chr8:49647907-49647957	AG10803	skin:	n/a
47	chr8:49647907-49647957	HEEpiC	esophagus:	n/a
48	chr8:49647907-49647957	Hepatocyte	liver:	n/a
49	chr8:49647907-49647957	NB4	blood:	n/a
50	chr8:49647907-49647957	AG09309	skin:	n/a

No data

Variant related genes	Relation type
EFCAB1	TF binding region
EFCAB1	CpG island

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10957199	1.00[YRI][hapmap]
rs12548278	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs13251991	1.00[YRI][hapmap]
rs1482262	1.00[YRI][hapmap]
rs16939055	1.00[YRI][hapmap]
rs35182554	0.89[ASN][1000 genomes]
rs4873289	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6415598	0.81[EUR][1000 genomes]
rs900237	1.00[YRI][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3750259	EFCAB1	cis	Esophagus Mucosa	GTEx
rs3750259	EFCAB1	cis	Esophagus Muscularis	GTEx
rs3750259	EFCAB1	cis	brain	BrainEAC
rs3750259	EFCAB1	cis	frontal cortex	BrainEAC
rs3750259	EFCAB1	cis	Nerve Tibial	GTEx
rs3750259	EFCAB1	cis	temporal cortex	BrainEAC
rs3750259	EFCAB1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49647000-49648000	Active TSS	Brain Anterior Caudate	brain
2	chr8:49647200-49648000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr8:49647200-49648000	Enhancers	Fetal Brain Male	brain
4	chr8:49647200-49648200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
5	chr8:49647200-49648200	Active TSS	Fetal Kidney	kidney
6	chr8:49647200-49648200	Active TSS	NHLF	lung
7	chr8:49647200-49648400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr8:49647200-49648400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
9	chr8:49647200-49648600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:49647400-49648000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:49647400-49648000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr8:49647400-49648000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:49647400-49648000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:49647400-49648000	Active TSS	Muscle Satellite Cultured Cells	--
15	chr8:49647400-49648000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr8:49647400-49648000	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr8:49647400-49648000	Active TSS	NHDF-Ad	bronchial
18	chr8:49647400-49648000	Active TSS	Osteobl	bone
19	chr8:49647400-49648200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr8:49647400-49648200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:49647400-49648200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:49647400-49648200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr8:49647400-49648200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:49647400-49648200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr8:49647400-49648200	Active TSS	Brain Substantia Nigra	brain
26	chr8:49647400-49648200	Active TSS	Colonic Mucosa	Colon
27	chr8:49647400-49648200	Active TSS	Duodenum Mucosa	Duodenum
28	chr8:49647400-49648200	Active TSS	Fetal Brain Female	brain
29	chr8:49647400-49648200	Active TSS	Rectal Smooth Muscle	rectum
30	chr8:49647400-49648400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr8:49647400-49648400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:49647400-49648400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:49647400-49648400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr8:49647400-49648400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr8:49647400-49648400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr8:49647400-49648400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:49647400-49648400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr8:49647400-49648400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr8:49647400-49648400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
40	chr8:49647400-49648400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr8:49647400-49648400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr8:49647400-49648400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr8:49647400-49648400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
44	chr8:49647400-49648400	Flanking Active TSS	Pancreas	Pancrea
45	chr8:49647400-49648400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr8:49647400-49648400	Flanking Active TSS	HMEC	breast
47	chr8:49647400-49648400	Active TSS	HSMM	muscle
48	chr8:49647400-49648600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr8:49647400-49648600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
50	chr8:49647400-49648600	Enhancers	Spleen	Spleen

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