Variant report

Variant	rs3784789
Chromosome Location	chr15:75082552-75082553
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	TAF1	chr15:75082219-75082685	GM12878	blood:	n/a	n/a
2	SPI1	chr15:75082302-75082738	GM12891	blood:	n/a	chr15:75082549-75082562
3	TCF12	chr15:75082267-75082676	GM12878	blood:	n/a	n/a
4	CUX1	chr15:75082027-75083312	GM12878	blood:	n/a	n/a
5	EGR1	chr15:75082417-75082712	GM12878	blood:	n/a	chr15:75082595-75082617
6	RELA	chr15:75078968-75083276	GM18951	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
7	POLR2A	chr15:75077574-75083240	GM19193	blood:	n/a	n/a
8	NFATC1	chr15:75079098-75082965	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75078871-75082774	GM12891	blood:	n/a	n/a
10	ATF2	chr15:75082185-75083362	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:75078541-75083313	GM12892	blood:	n/a	n/a
12	POU2F2	chr15:75082282-75082713	GM12878	blood:	n/a	n/a
13	FOXM1	chr15:75082238-75083270	GM12878	blood:	n/a	n/a
14	USF2	chr15:75082425-75082848	GM12878	blood:	n/a	chr15:75082678-75082687 chr15:75082678-75082687 chr15:75082679-75082688
15	ELF1	chr15:75082074-75083331	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:75078876-75083272	GM12878	blood:	n/a	n/a
17	BRCA1	chr15:75082230-75082620	GM12878	blood:	n/a	n/a
18	RELA	chr15:75078928-75083342	GM18505	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440
19	BCL11A	chr15:75082383-75082716	GM12878	blood:	n/a	n/a
20	PAX5	chr15:75082350-75082737	GM12878	blood:	n/a	n/a
21	PAX5	chr15:75082405-75082906	GM12878	blood:	n/a	n/a
22	POU2F2	chr15:75078933-75083247	GM12878	blood:	n/a	chr15:75081175-75081185 chr15:75081175-75081185 chr15:75081174-75081186 chr15:75081172-75081187 chr15:75081176-75081183 chr15:75081168-75081189 chr15:75081174-75081184 chr15:75081175-75081183 chr15:75081175-75081184 chr15:75081170-75081188 chr15:75081173-75081184
23	POLR2A	chr15:75078956-75083263	GM12892	blood:	n/a	n/a
24	CHD2	chr15:75079257-75083224	GM12878	blood:	n/a	n/a
25	MXI1	chr15:75082128-75083223	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:75079535-75083264	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:75076731-75083396	GM12892	blood:	n/a	n/a
28	EP300	chr15:75082314-75082907	GM12878	blood:	n/a	n/a
29	SPI1	chr15:75082327-75082705	GM12891	blood:	n/a	chr15:75082549-75082562
30	EBF1	chr15:75082151-75083357	GM12878	blood:	n/a	n/a
31	RCOR1	chr15:75082302-75082794	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:75072814-75083294	GM19099	blood:	n/a	n/a
33	POLR2A	chr15:75072482-75083351	GM12878	blood:	n/a	n/a
34	PAX5	chr15:75082317-75082856	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:75078570-75083275	GM18505	blood:	n/a	n/a
36	ELF1	chr15:75082218-75082988	GM12878	blood:	n/a	n/a
37	MAZ	chr15:75079154-75082852	GM12878	blood:	n/a	chr15:75082678-75082687 chr15:75081867-75081877
38	RUNX3	chr15:75082147-75083632	GM12878	blood:	n/a	chr15:75083175-75083190
39	BCLAF1	chr15:75078912-75083306	GM12878	blood:	n/a	chr15:75081349-75081362 chr15:75080342-75080351
40	IRF4	chr15:75082243-75082848	GM12878	blood:	n/a	n/a
41	BCL11A	chr15:75082344-75082973	GM12878	blood:	n/a	n/a
42	BCLAF1	chr15:75082030-75082820	GM12878	blood:	n/a	n/a
43	MTA3	chr15:75078545-75083429	GM12878	blood:	n/a	n/a
44	BHLHE40	chr15:75082296-75083484	GM12878	blood:	n/a	chr15:75082678-75082687 chr15:75082678-75082687 chr15:75082679-75082688
45	TBP	chr15:75082287-75083305	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:75078927-75082956	Raji	blood:	n/a	n/a
47	ELK1	chr15:75082225-75082746	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:75078866-75083275	HL-60	blood:	n/a	n/a
49	CHD1	chr15:75082260-75083558	IMR90	lung:	n/a	n/a
50	RELA	chr15:75079480-75083317	GM19099	blood:	n/a	chr15:75081431-75081440 chr15:75081431-75081440

No.	Distal block	Cell Line	Cell type
1	chr15:74928882..74931571-chr15:75081433..75082999,2	MCF-7	breast:
2	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
3	chr15:75081397..75085815-chr15:75182279..75185381,4	MCF-7	breast:
4	chr15:75081298..75083220-chr15:75099537..75101097,2	K562	blood:
5	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
6	chr15:75081235..75085402-chr15:75108223..75111318,4	MCF-7	breast:
7	chr15:75079725..75083728-chr15:75089989..75095483,10	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
MIR4513	TF binding region
ENSG00000261606	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000140506	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072507	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072508	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636952	0.95[CEU][hapmap]
rs12591513	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903541	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.87[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917376	0.94[ASN][1000 genomes]
rs1378940	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470890	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472304	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.89[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765066	0.87[CEU][hapmap]
rs4886410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006566	0.80[AMR][1000 genomes]
rs62006567	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3784789	SCAMP5	cis	Artery Tibial	GTEx
rs3784789	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs3784789	SCAMP5	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75075600-75083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr15:75076400-75083200	Enhancers	Colon Smooth Muscle	Colon
3	chr15:75076400-75083400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr15:75076400-75083400	Genic enhancers	Fetal Stomach	stomach
5	chr15:75076400-75083400	Enhancers	Right Ventricle	heart
6	chr15:75076400-75084200	Enhancers	Spleen	Spleen
7	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
8	chr15:75076600-75082600	Genic enhancers	NHEK	skin
9	chr15:75076600-75082800	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr15:75076600-75083400	Enhancers	Right Atrium	heart
11	chr15:75076600-75083400	Enhancers	HMEC	breast
12	chr15:75076600-75084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:75076800-75083200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:75077600-75083000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:75077600-75083000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:75077600-75083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:75077800-75084400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:75078000-75083400	Enhancers	Placenta	Placenta
20	chr15:75078000-75083400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr15:75078000-75083600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr15:75078000-75084200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:75078000-75085600	Enhancers	NHDF-Ad	bronchial
24	chr15:75078200-75083200	Enhancers	Gastric	stomach
25	chr15:75078200-75083400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr15:75078200-75083600	Enhancers	Small Intestine	intestine
27	chr15:75078200-75084400	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr15:75078600-75082800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr15:75078600-75083000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr15:75078600-75083200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:75078600-75085000	Enhancers	NHLF	lung
32	chr15:75078800-75082800	Enhancers	NH-A	brain
33	chr15:75078800-75083200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:75078800-75083400	Enhancers	Brain Angular Gyrus	brain
35	chr15:75078800-75084600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:75079000-75083400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr15:75079200-75082800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:75079200-75083200	Enhancers	A549	lung
39	chr15:75079200-75083600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:75079400-75093800	Weak transcription	Aorta	Aorta
41	chr15:75079800-75082800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:75079800-75083400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr15:75080000-75082600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr15:75080000-75082600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr15:75080000-75082800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr15:75080000-75083000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:75080000-75083000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr15:75080000-75083400	Enhancers	Fetal Lung	lung
49	chr15:75080000-75084000	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr15:75080200-75084600	Weak transcription	Psoas Muscle	Psoas

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