Variant report

Variant	rs3809542
Chromosome Location	chr15:74610713-74610714
allele	A/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	SPI1	chr15:74610688-74610909	K562	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815
2	SPI1	chr15:74610281-74611010	GM12878	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815 chr15:74610343-74610350
3	SPI1	chr15:74610693-74610990	GM12878	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815
4	ZNF263	chr15:74610153-74610769	HEK293-T-REx	kidney:	n/a	chr15:74610482-74610503 chr15:74610640-74610649
5	EBF1	chr15:74610698-74611121	GM12878	blood:	n/a	chr15:74610887-74610897 chr15:74610885-74610898 chr15:74610887-74610896 chr15:74610886-74610897 chr15:74610887-74610896
6	EBF1	chr15:74610659-74611080	GM12878	blood:	n/a	chr15:74610887-74610897 chr15:74610885-74610898 chr15:74610887-74610896 chr15:74610886-74610897 chr15:74610887-74610896
7	SPI1	chr15:74610589-74610989	GM12891	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815
8	ELF1	chr15:74610711-74611271	GM12878	blood:	n/a	n/a
9	SPI1	chr15:74610609-74611054	HL-60	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815
10	EBF1	chr15:74610701-74611078	GM12878	blood:	n/a	chr15:74610887-74610897 chr15:74610885-74610898 chr15:74610887-74610896 chr15:74610886-74610897 chr15:74610887-74610896
11	SPI1	chr15:74610653-74610993	GM12891	blood:	n/a	chr15:74610801-74610814 chr15:74610804-74610813 chr15:74610802-74610815

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:74610683-74610733	GM12891	blood:	n/a
2	chr15:74610683-74610733	HEEpiC	esophagus:	n/a
3	chr15:74610683-74610733	HMEC	breast:	n/a
4	chr15:74610683-74610733	HEK293	kidney:	embryo
5	chr15:74610683-74610733	HCT-116	colon:	n/a
6	chr15:74610683-74610733	NH-A	brain:	n/a
7	chr15:74610683-74610733	HRE	kidney:	n/a
8	chr15:74610683-74610733	GM06990	blood:	n/a
9	chr15:74610683-74610733	ProgFib	skin:	n/a
10	chr15:74610683-74610733	H1-hESC	embryonic stem cell:	embryo
11	chr15:74610683-74610733	ovcar-3	ovarian:	n/a
12	chr15:74610683-74610733	NHDF-neo	bronchial:	n/a
13	chr15:74610683-74610733	A549	lung:	n/a
14	chr15:74610683-74610733	HL-60	blood:	n/a
15	chr15:74610683-74610733	K562	blood:	n/a
16	chr15:74610683-74610733	Hepatocyte	liver:	n/a
17	chr15:74610683-74610733	GM12892	blood:	n/a
18	chr15:74610683-74610733	LNCaP	prostate:	n/a
19	chr15:74610683-74610733	BE2_C	brain:	n/a
20	chr15:74610683-74610733	HAEpiC	amniotic membrane:	n/a
21	chr15:74610683-74610733	NHBE	bronchial:	n/a
22	chr15:74610683-74610733	SK-N-SH	brain:	n/a
23	chr15:74610683-74610733	HUVEC	blood vessel:	n/a
24	chr15:74610683-74610733	HepG2	liver:	n/a
25	chr15:74610683-74610733	RPTEC	kidney:	n/a
26	chr15:74610683-74610733	SK-N-MC	brain:	n/a
27	chr15:74610683-74610733	SK-N-SH_RA	brain:	n/a
28	chr15:74610683-74610733	AG04450	lung:	fetal
29	chr15:74610683-74610733	HCPEpiC	choroid plexus:	n/a
30	chr15:74610683-74610733	HPAEpiC	pulmonary alveolar:	n/a
31	chr15:74610683-74610733	MCF10A-Er-Src	breast:	n/a
32	chr15:74610683-74610733	NB4	blood:	n/a
33	chr15:74610683-74610733	T-47D	breast:	n/a
34	chr15:74610683-74610733	AG04449	skin:	fetal
35	chr15:74610683-74610733	PFSK-1	brain:	n/a
36	chr15:74610683-74610733	PANC-1	pancreas:	n/a
37	chr15:74610683-74610733	CMK	blood:	n/a
38	chr15:74610683-74610733	HCM	heart:	n/a
39	chr15:74610683-74610733	GM19239	blood:	n/a
40	chr15:74610683-74610733	MCF-7	breast:	n/a
41	chr15:74610683-74610733	HRCEpiC	kidney:	n/a
42	chr15:74610683-74610733	IMR90	lung:	fetal
43	chr15:74610683-74610733	HIPEpiC	eye:	n/a
44	chr15:74610683-74610733	GM12878	blood:	n/a
45	chr15:74610683-74610733	HNPCEpiC	eye:	n/a
46	chr15:74610683-74610733	NT2-D1	testis:	n/a
47	chr15:74610683-74610733	Caco-2	colon:	n/a
48	chr15:74610683-74610733	PrEC	prostate:	n/a
49	chr15:74610683-74610733	SAEC	small airway:	n/a
50	chr15:74610683-74610733	HCF	heart:	n/a

Variant related genes	Relation type
CCDC33	TF binding region
CCDC33	CpG island

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17515476	0.80[ASN][1000 genomes]
rs41553612	0.80[ASN][1000 genomes]
rs41553712	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs41563614	0.80[ASN][1000 genomes]
rs55766734	0.98[ASN][1000 genomes]
rs56308802	1.00[AFR][1000 genomes]
rs59984854	0.84[AFR][1000 genomes]
rs60226645	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs60852398	0.81[AFR][1000 genomes]
rs7163952	0.80[ASN][1000 genomes]
rs7175214	0.80[ASN][1000 genomes]
rs74023479	0.80[ASN][1000 genomes]
rs74023491	1.00[AFR][1000 genomes]
rs74023494	0.95[AFR][1000 genomes]
rs74023496	0.92[AFR][1000 genomes]
rs74023499	0.84[AFR][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	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74603000-74610800	Enhancers	Fetal Brain Male	brain
2	chr15:74604200-74613400	Enhancers	Placenta	Placenta
3	chr15:74604400-74613200	Enhancers	Fetal Thymus	thymus
4	chr15:74604800-74623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:74605200-74613400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr15:74605400-74611200	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:74606200-74612600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:74606200-74613400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:74606400-74613400	Enhancers	Fetal Muscle Leg	muscle
10	chr15:74606600-74611200	Enhancers	Brain Germinal Matrix	brain
11	chr15:74606600-74613400	Enhancers	Fetal Brain Female	brain
12	chr15:74607000-74611400	Enhancers	NH-A	brain
13	chr15:74607000-74613000	Enhancers	Primary hematopoietic stem cells	blood
14	chr15:74607200-74611600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:74607200-74611800	Enhancers	Left Ventricle	heart
16	chr15:74607200-74612000	Enhancers	Right Ventricle	heart
17	chr15:74607200-74612600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:74607200-74613000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:74607200-74613200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:74607200-74613400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr15:74607400-74613200	Enhancers	Adipose Nuclei	Adipose
22	chr15:74607600-74611600	Enhancers	HSMMtube	muscle
23	chr15:74607600-74613400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:74607800-74612000	Enhancers	NHLF	lung
25	chr15:74607800-74613000	Enhancers	Fetal Stomach	stomach
26	chr15:74608000-74612600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:74608000-74613000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:74608200-74611000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:74608200-74611200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:74608200-74613200	Enhancers	GM12878-XiMat	blood
31	chr15:74608400-74611400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:74608400-74613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:74608600-74611600	Weak transcription	Primary T cells from cord blood	blood
34	chr15:74608600-74611800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr15:74608800-74611600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:74608800-74612200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:74608800-74613200	Enhancers	Stomach Smooth Muscle	stomach
38	chr15:74609000-74610800	Weak transcription	Fetal Heart	heart
39	chr15:74609200-74613000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr15:74609400-74611000	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:74609600-74610800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:74609600-74611400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:74609600-74612000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr15:74609600-74612200	Enhancers	Stomach Mucosa	stomach
45	chr15:74609600-74612800	Enhancers	Fetal Intestine Small	intestine
46	chr15:74609600-74613000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr15:74609600-74613200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:74609800-74611000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:74609800-74611000	Enhancers	A549	lung
50	chr15:74609800-74611200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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