Variant report

Variant	rs2290574
Chromosome Location	chr15:75135447-75135448
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	TAF1	chr15:75134875-75136001	ECC-1	luminal epithelium:	n/a	n/a
2	USF1	chr15:75135304-75135872	K562	blood:	n/a	n/a
3	CTCF	chr15:75135440-75135590	GM12866	blood:	n/a	chr15:75135547-75135560
4	BCL3	chr15:75135032-75135945	GM12878	blood:	n/a	chr15:75135784-75135793 chr15:75135479-75135492 chr15:75135594-75135607
5	RAD21	chr15:75135342-75135833	SK-N-SH_RA	brain:	n/a	chr15:75135646-75135660 chr15:75135538-75135548
6	POLR2A	chr15:75134868-75135990	MCF-7	breast:	n/a	n/a
7	CTCF	chr15:75135378-75135772	A549	lung:	n/a	chr15:75135547-75135560
8	CTCF	chr15:75135300-75135886	H1-hESC	embryonic stem cell:	n/a	chr15:75135547-75135560 chr15:75135768-75135781
9	POLR2A	chr15:75134600-75136938	SK-N-MC	brain:	n/a	n/a
10	SP4	chr15:75134813-75135621	H1-hESC	embryonic stem cell:	n/a	n/a
11	ELF1	chr15:75135257-75135780	K562	blood:	n/a	n/a
12	REST	chr15:75134466-75136193	H1-neurons	neurons:	n/a	n/a
13	HA-E2F1	chr15:75135230-75135891	Hela-S3	cervix:	n/a	chr15:75135786-75135795
14	POLR2A	chr15:75134854-75135936	Hela-S3	cervix:	n/a	n/a
15	CBX3	chr15:75135439-75135874	K562	blood:	n/a	n/a
16	MYC	chr15:75135004-75136097	K562	blood:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784
17	CREB1	chr15:75135297-75136022	GM12878	blood:	n/a	n/a
18	MAX	chr15:75134929-75136074	H1-hESC	embryonic stem cell:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784
19	POLR2A	chr15:75134832-75136029	HUVEC	blood vessel:	n/a	n/a
20	GABPA	chr15:75134950-75135888	MCF-7	breast:	n/a	chr15:75135483-75135492 chr15:75135454-75135468 chr15:75135548-75135557 chr15:75135780-75135789
21	MAZ	chr15:75135036-75135891	Hela-S3	cervix:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784
22	POLR2A	chr15:75135143-75136036	GM12891	blood:	n/a	n/a
23	MAX	chr15:75134844-75136003	H1-hESC	embryonic stem cell:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784
24	CTCF	chr15:75135241-75135824	GM19239	blood:	n/a	chr15:75135547-75135560 chr15:75135768-75135781
25	CTCF	chr15:75135376-75135827	A549	lung:	n/a	chr15:75135547-75135560 chr15:75135768-75135781
26	JUND	chr15:75135350-75135886	K562	blood:	n/a	chr15:75135549-75135558 chr15:75135506-75135515
27	POLR2A	chr15:75135021-75135743	HepG2	liver:	n/a	n/a
28	YY1	chr15:75135036-75135752	ECC-1	luminal epithelium:	n/a	chr15:75135454-75135468 chr15:75135540-75135554
29	MEF2A	chr15:75135367-75135937	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr15:75135180-75135896	A549	lung:	n/a	n/a
31	PML	chr15:75134957-75136143	GM12878	blood:	n/a	n/a
32	CTCF	chr15:75135376-75135830	HepG2	liver:	n/a	chr15:75135547-75135560 chr15:75135768-75135781
33	RAD21	chr15:75135316-75135722	HepG2	liver:	n/a	chr15:75135646-75135660 chr15:75135538-75135548
34	USF1	chr15:75135445-75135817	A549	lung:	n/a	n/a
35	SIN3AK20	chr15:75135352-75135925	SK-N-SH	brain:	n/a	n/a
36	ZBTB7A	chr15:75134896-75135966	ECC-1	luminal epithelium:	n/a	n/a
37	PAX5	chr15:75135100-75135926	GM12892	blood:	n/a	chr15:75135458-75135467 chr15:75135464-75135473
38	GATA3	chr15:75135032-75136048	A549	lung:	n/a	n/a
39	POLR2A	chr15:75134963-75135920	HEK293	kidney:	n/a	n/a
40	POLR2A	chr15:75135027-75135947	A549	lung:	n/a	n/a
41	USF1	chr15:75135427-75135844	A549	lung:	n/a	n/a
42	USF1	chr15:75135346-75136013	HCT-116	colon:	n/a	n/a
43	JUND	chr15:75135413-75135634	H1-hESC	embryonic stem cell:	n/a	chr15:75135549-75135558 chr15:75135506-75135515
44	USF1	chr15:75135378-75135966	K562	blood:	n/a	n/a
45	TBP	chr15:75135010-75135927	K562	blood:	n/a	n/a
46	MAX	chr15:75134836-75136124	HCT-116	colon:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784
47	POLR2A	chr15:75134947-75136094	HL-60	blood:	n/a	n/a
48	TEAD4	chr15:75135056-75135662	A549	lung:	n/a	n/a
49	POLR2A	chr15:75135114-75135795	Gliobla	brain:	n/a	n/a
50	MYC	chr15:75134891-75136063	K562	blood:	n/a	chr15:75135660-75135675 chr15:75135765-75135774 chr15:75135660-75135669 chr15:75135661-75135671 chr15:75135774-75135784

No.	Distal block	Cell Line	Cell type
1	chr15:74926089..74928915-chr15:75133890..75136502,2	MCF-7	breast:
2	chr15:75073852..75074625-chr15:75135150..75135967,3	MCF-7	breast:
3	chr15:75090773..75092693-chr15:75133525..75135797,3	K562	blood:
4	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
5	chr15:75115272..75120114-chr15:75130983..75135707,7	K562	blood:
6	chr15:74906653..74908395-chr15:75135147..75137390,2	K562	blood:
7	chr15:74906299..74909390-chr15:75133726..75137690,7	MCF-7	breast:
8	chr15:75133989..75136127-chr15:75187296..75189781,2	K562	blood:
9	chr15:74832995..74834922-chr15:75133837..75135469,2	K562	blood:
10	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
11	chr15:75134990..75135563-chr20:30194262..30195030,2	Hela-S3	cervix:
12	chr15:75133947..75135664-chr15:75246136..75249268,3	MCF-7	breast:
13	chr15:75091193..75092930-chr15:75133955..75135797,2	K562	blood:
14	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
15	chr15:75105168..75109047-chr15:75134120..75137766,4	K562	blood:
16	chr15:75134593..75136676-chr15:75247766..75251919,4	MCF-7	breast:
17	chr15:75134997..75135662-chr6:108279356..108279933,2	HCT-116	colon:
18	chr15:75072228..75074857-chr15:75134119..75137193,5	K562	blood:
19	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
20	chr15:75133683..75136875-chr15:75181140..75184004,7	K562	blood:
21	chr15:75135427..75140750-chr15:75141950..75147054,10	K562	blood:
22	chr15:75133406..75136691-chr15:75228046..75231533,6	MCF-7	breast:
23	chr15:75090900..75093717-chr15:75134239..75137508,3	MCF-7	breast:
24	chr11:65190032..65190914-chr15:75134891..75135778,2	Hela-S3	cervix:
25	chr15:75133950..75137156-chr15:75180779..75184661,9	MCF-7	breast:
26	chr15:75134051..75136456-chr15:75197581..75199707,3	K562	blood:
27	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
28	chr15:75132852..75135633-chr15:75196341..75200571,3	K562	blood:
29	chr15:75133790..75137554-chr15:75195204..75200578,14	MCF-7	breast:
30	chr15:75132595..75137581-chr15:75190842..75194074,4	K562	blood:
31	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
32	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
33	chr15:75134794..75137581-chr15:75190842..75193156,3	K562	blood:
34	chr15:75135336..75137971-chr15:75192308..75194100,2	MCF-7	breast:
35	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:
36	chr15:75072623..75074857-chr15:75134348..75137142,2	K562	blood:

Variant related genes	Relation type
ULK3	TF binding region
ENSG00000264386	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000179361	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000179151	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000025796	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1869959	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2305668	0.80[ASN][1000 genomes]
rs4886613	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886615	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180432	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936228	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936229	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936230	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
4	nsv904382	chr15:75129594-75140854	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569992	chr15:75132319-75137868	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2290574	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs2290574	ULK3	cis	Whole Blood	GTEx
rs2290574	MPI	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75134200-75136000	Active TSS	Brain Anterior Caudate	brain
2	chr15:75134400-75136000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:75134400-75136200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:75134400-75136200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr15:75134400-75136400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:75134600-75135800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:75134600-75136000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:75134600-75136200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr15:75134600-75136200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:75134600-75136200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:75134600-75136600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr15:75134600-75136600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr15:75134800-75135600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr15:75134800-75135600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:75134800-75135600	Active TSS	Hela-S3	cervix
16	chr15:75134800-75135800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:75134800-75135800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:75134800-75135800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr15:75134800-75135800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:75134800-75135800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:75134800-75135800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:75134800-75135800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:75134800-75135800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:75134800-75135800	Active TSS	Brain Cingulate Gyrus	brain
25	chr15:75134800-75135800	Active TSS	Colon Smooth Muscle	Colon
26	chr15:75134800-75135800	Active TSS	Duodenum Mucosa	Duodenum
27	chr15:75134800-75135800	Active TSS	Esophagus	oesophagus
28	chr15:75134800-75135800	Active TSS	Fetal Intestine Large	intestine
29	chr15:75134800-75135800	Active TSS	Pancreas	Pancrea
30	chr15:75134800-75135800	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:75134800-75135800	Active TSS	A549	lung
32	chr15:75134800-75135800	Active TSS	GM12878-XiMat	blood
33	chr15:75134800-75135800	Active TSS	HSMMtube	muscle
34	chr15:75134800-75135800	Active TSS	NHDF-Ad	bronchial
35	chr15:75134800-75135800	Active TSS	NHLF	lung
36	chr15:75134800-75136000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr15:75134800-75136000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr15:75134800-75136000	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr15:75134800-75136000	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr15:75134800-75136000	Active TSS	Aorta	Aorta
41	chr15:75134800-75136000	Active TSS	Fetal Lung	lung
42	chr15:75134800-75136000	Active TSS	Gastric	stomach
43	chr15:75134800-75136000	Active TSS	Left Ventricle	heart
44	chr15:75134800-75136000	Active TSS	Ovary	ovary
45	chr15:75134800-75136200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr15:75134800-75136200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr15:75134800-75136200	Active TSS	Fetal Brain Female	brain
48	chr15:75134800-75136200	Active TSS	Fetal Kidney	kidney
49	chr15:75134800-75136400	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr15:75134800-75136400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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