Variant report

Variant	rs4886629
Chromosome Location	chr15:75072558-75072559
allele	C/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	BHLHE40	chr15:75072484-75072856	GM12878	blood:	n/a	n/a
2	MAFF	chr15:75072547-75072897	K562	blood:	n/a	chr15:75072711-75072729
3	FOXM1	chr15:75072500-75073080	GM12878	blood:	n/a	n/a
4	MAFK	chr15:75072551-75072871	HepG2	liver:	n/a	n/a
5	RUNX3	chr15:75072495-75074433	GM12878	blood:	n/a	n/a
6	HNF4A	chr15:75072181-75072675	HepG2	liver:	n/a	chr15:75072364-75072379
7	GATA2	chr15:75072479-75072831	SH-SY5Y	brain:	n/a	n/a
8	CUX1	chr15:75072493-75072762	K562	blood:	n/a	n/a
9	POLR2A	chr15:75072482-75083351	GM12878	blood:	n/a	n/a
10	RXRA	chr15:75072172-75072728	HepG2	liver:	n/a	n/a
11	HNF4A	chr15:75072227-75072623	HepG2	liver:	n/a	chr15:75072364-75072379
12	POLR2A	chr15:75072317-75074453	SK-N-MC	brain:	n/a	n/a
13	MYC	chr15:75072545-75072880	K562	blood:	n/a	n/a
14	POLR2A	chr15:75072246-75074809	GM12891	blood:	n/a	n/a
15	FOXA2	chr15:75072211-75072596	HepG2	liver:	n/a	n/a
16	FOXA1	chr15:75072189-75072723	HepG2	liver:	n/a	n/a
17	FOXA1	chr15:75072229-75072643	HepG2	liver:	n/a	n/a
18	MAZ	chr15:75072490-75072905	K562	blood:	n/a	n/a
19	HNF4A	chr15:75072203-75072586	HepG2	liver:	n/a	chr15:75072364-75072379
20	RCOR1	chr15:75072430-75072974	K562	blood:	n/a	n/a
21	TBL1XR1	chr15:75072544-75072858	K562	blood:	n/a	n/a
22	PML	chr15:75072475-75074422	GM12878	blood:	n/a	chr15:75074213-75074221
23	ZNF143	chr15:75072408-75073143	GM12878	blood:	n/a	chr15:75072545-75072564 chr15:75073067-75073085
24	RELA	chr15:75072551-75074499	GM18505	blood:	n/a	n/a
25	FOXA1	chr15:75072160-75072600	HepG2	liver:	n/a	n/a
26	IRF1	chr15:75072517-75072889	K562	blood:	n/a	chr15:75072647-75072661 chr15:75072651-75072661 chr15:75072648-75072662 chr15:75072643-75072663 chr15:75072651-75072665 chr15:75072649-75072663
27	MAFK	chr15:75072556-75072864	HepG2	liver:	n/a	n/a
28	HNF4G	chr15:75072097-75072630	HepG2	liver:	n/a	chr15:75072363-75072378
29	MTA3	chr15:75072205-75074428	GM12878	blood:	n/a	n/a
30	MYBL2	chr15:75072149-75072913	HepG2	liver:	n/a	n/a
31	NFATC1	chr15:75072558-75073072	GM12878	blood:	n/a	n/a
32	HNF4G	chr15:75072171-75072581	HepG2	liver:	n/a	chr15:75072363-75072378
33	ZNF143	chr15:75072399-75072954	K562	blood:	n/a	chr15:75072545-75072564
34	HDAC2	chr15:75072114-75072567	HepG2	liver:	n/a	chr15:75072407-75072415
35	POLR2A	chr15:75072548-75073891	HL-60	blood:	n/a	n/a
36	GATA1	chr15:75072411-75072966	PBDE	blood:	n/a	n/a
37	RXRA	chr15:75072187-75072614	HepG2	liver:	n/a	n/a
38	MAFK	chr15:75072535-75072861	K562	blood:	n/a	n/a
39	GATA2	chr15:75072464-75072850	K562	blood:	n/a	n/a
40	JUND	chr15:75072482-75072803	K562	blood:	n/a	chr15:75072599-75072608
41	NFIC	chr15:75072464-75074340	GM12878	blood:	n/a	n/a
42	EP300	chr15:75072162-75072822	HepG2	liver:	n/a	n/a
43	ARID3A	chr15:75072165-75072775	HepG2	liver:	n/a	n/a
44	RUNX3	chr15:75072497-75074435	GM12878	blood:	n/a	n/a
45	MAX	chr15:75072553-75072934	K562	blood:	n/a	n/a
46	GATA1	chr15:75072113-75073204	K562	blood:	n/a	n/a
47	GATA3	chr15:75072480-75072693	MCF-7	breast:	n/a	n/a
48	POLR2A	chr15:75072430-75072877	SK-N-MC	brain:	n/a	n/a
49	MAFF	chr15:75072520-75072908	HepG2	liver:	n/a	chr15:75072711-75072729
50	SP1	chr15:75072188-75072850	HepG2	liver:	n/a	chr15:75072547-75072560 chr15:75072522-75072531

No.	Distal block	Cell Line	Cell type
1	chr15:75071180..75073699-chr15:75308688..75311602,2	MCF-7	breast:
2	chr15:75071239..75073598-chr15:75247193..75248970,3	K562	blood:
3	chr15:75070902..75072861-chr15:75132402..75135175,2	MCF-7	breast:
4	chr15:75072512..75079183-chr15:75180576..75186728,11	MCF-7	breast:
5	chr15:74908350..74910118-chr15:75071323..75073781,2	MCF-7	breast:
6	chr15:75071971..75073821-chr15:75084189..75086951,2	K562	blood:
7	chr15:75072228..75074857-chr15:75134119..75137193,5	K562	blood:
8	chr15:75072350..75078841-chr15:75107920..75114107,12	MCF-7	breast:
9	chr15:75071239..75073598-chr15:75247367..75248970,2	K562	blood:
10	chr15:75072261..75077453-chr15:75091040..75094267,5	K562	blood:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11072502	0.80[EUR][1000 genomes]
rs11072509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634474	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636952	0.83[CEU][hapmap]
rs12441505	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442901	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591078	0.82[EUR][1000 genomes]
rs1350193	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1378938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1543927	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs2071501	0.87[JPT][hapmap]
rs2168519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2301249	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472299	0.82[CEU][hapmap]
rs3784790	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935077	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886406	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs4886619	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7162232	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176022	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7180484	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72730503	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762551	0.82[CEU][hapmap]
rs8033381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9210	0.86[CEU][hapmap]
rs936226	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs936230	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4886629	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs4886629	ULK3	cis	Whole Blood	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75065600-75072600	Enhancers	Primary hematopoietic stem cells	blood
2	chr15:75065600-75073200	Weak transcription	Brain Angular Gyrus	brain
3	chr15:75065600-75073600	Enhancers	Fetal Intestine Large	intestine
4	chr15:75065600-75073600	Enhancers	Fetal Intestine Small	intestine
5	chr15:75065800-75072800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:75066200-75073000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:75066400-75072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:75066600-75072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:75067200-75072800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:75067400-75074200	Enhancers	Stomach Mucosa	stomach
11	chr15:75068000-75073200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:75068800-75073400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr15:75069000-75072600	Enhancers	Liver	Liver
14	chr15:75069000-75072800	Enhancers	Thymus	Thymus
15	chr15:75069200-75072800	Enhancers	K562	blood
16	chr15:75069600-75072600	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:75069600-75073800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:75069800-75072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr15:75069800-75072800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:75069800-75073000	Weak transcription	Gastric	stomach
21	chr15:75070000-75072800	Weak transcription	Fetal Brain Female	brain
22	chr15:75070000-75072800	Weak transcription	NHDF-Ad	bronchial
23	chr15:75070000-75073000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:75070000-75073200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:75070000-75073200	Weak transcription	Osteobl	bone
26	chr15:75070000-75073800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:75070200-75072600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:75070200-75072600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:75070200-75072600	Enhancers	Fetal Thymus	thymus
30	chr15:75070200-75072800	Enhancers	Primary B cells from peripheral blood	blood
31	chr15:75070200-75072800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:75070200-75073200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:75070200-75073200	Weak transcription	HSMMtube	muscle
34	chr15:75070200-75073400	Weak transcription	HSMM	muscle
35	chr15:75070200-75073600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:75070400-75072800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr15:75070400-75072800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:75070400-75072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:75070400-75073000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr15:75070400-75073000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:75070400-75073000	Weak transcription	Right Ventricle	heart
42	chr15:75070400-75073000	Enhancers	Dnd41	blood
43	chr15:75070400-75073200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:75070400-75073200	Weak transcription	Brain Anterior Caudate	brain
45	chr15:75070400-75073200	Enhancers	Fetal Heart	heart
46	chr15:75070400-75073200	Weak transcription	Left Ventricle	heart
47	chr15:75070400-75073400	Weak transcription	Right Atrium	heart
48	chr15:75070600-75072600	Weak transcription	Fetal Stomach	stomach
49	chr15:75070600-75072800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:75070600-75072800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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