Variant report

Variant	rs12905199
Chromosome Location	chr15:75070196-75070197
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	EBF1	chr15:75069053-75070594	GM12878	blood:	n/a	chr15:75070178-75070187 chr15:75070176-75070189 chr15:75069993-75070003 chr15:75070177-75070187 chr15:75069991-75070004 chr15:75069992-75070003 chr15:75069355-75069365 chr15:75069993-75070002
2	RELA	chr15:75069497-75070566	GM18505	blood:	n/a	n/a
3	EP300	chr15:75069684-75070267	GM12878	blood:	n/a	chr15:75069712-75069728
4	CEBPB	chr15:75069276-75070271	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:75069024-75070576	HL-60	blood:	n/a	n/a
6	MAZ	chr15:75069358-75070539	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:75069250-75070730	Raji	blood:	n/a	n/a
8	BCLAF1	chr15:75069034-75070213	GM12878	blood:	n/a	chr15:75069691-75069699
9	POLR2A	chr15:75069206-75070548	GM18505	blood:	n/a	n/a
10	POLR2A	chr15:75069101-75070634	GM12891	blood:	n/a	n/a
11	RUNX3	chr15:75069087-75070686	GM12878	blood:	n/a	n/a
12	MAX	chr15:75069570-75070583	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:75069443-75070573	GM18951	blood:	n/a	n/a
14	SMC3	chr15:75069706-75070454	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:75069268-75070336	GM12891	blood:	n/a	n/a
16	WRNIP1	chr15:75069246-75070403	GM12878	blood:	n/a	n/a
17	STAT5A	chr15:75068873-75070340	GM12878	blood:	n/a	chr15:75069984-75069996 chr15:75069144-75069151 chr15:75069202-75069210
18	EBF1	chr15:75069070-75070620	GM12878	blood:	n/a	chr15:75070178-75070187 chr15:75070176-75070189 chr15:75069993-75070003 chr15:75070177-75070187 chr15:75069991-75070004 chr15:75069992-75070003 chr15:75069355-75069365 chr15:75069993-75070002
19	POLR2A	chr15:75068864-75070645	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:75069088-75070635	GM12892	blood:	n/a	n/a
21	CHD2	chr15:75069412-75070273	GM12878	blood:	n/a	n/a
22	FOXM1	chr15:75069523-75070678	GM12878	blood:	n/a	n/a
23	BHLHE40	chr15:75069572-75070504	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:75068779-75070595	GM12878	blood:	n/a	n/a
25	SPI1	chr15:75069257-75070450	GM12878	blood:	n/a	chr15:75069849-75069862
26	NFIC	chr15:75069026-75070765	GM12878	blood:	n/a	chr15:75069282-75069298 chr15:75069488-75069505 chr15:75069270-75069298 chr15:75069756-75069784
27	CUX1	chr15:75069657-75070447	GM12878	blood:	n/a	n/a
28	POU2F2	chr15:75069444-75070609	GM12878	blood:	n/a	n/a
29	RELA	chr15:75069282-75070495	GM18951	blood:	n/a	n/a
30	TBP	chr15:75069687-75070579	GM12878	blood:	n/a	n/a
31	TAF1	chr15:75070033-75070415	GM12878	blood:	n/a	n/a
32	SPI1	chr15:75068953-75070721	HL-60	blood:	n/a	chr15:75069206-75069219 chr15:75069849-75069862
33	MTA3	chr15:75068882-75070259	GM12878	blood:	n/a	n/a
34	RUNX3	chr15:75069053-75070622	GM12878	blood:	n/a	n/a
35	PML	chr15:75068944-75070783	GM12878	blood:	n/a	n/a
36	RELA	chr15:75069374-75070577	GM19099	blood:	n/a	n/a
37	MTA3	chr15:75068806-75070779	GM12878	blood:	n/a	n/a
38	BCL3	chr15:75069364-75070316	GM12878	blood:	n/a	chr15:75069691-75069699
39	YY1	chr15:75069509-75070306	GM12892	blood:	n/a	chr15:75069755-75069766
40	POLR2A	chr15:75069236-75070687	GM19099	blood:	n/a	n/a
41	POLR2A	chr15:75069182-75070476	GM19193	blood:	n/a	n/a
42	ZNF384	chr15:75069781-75070749	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:75069110-75070647	GM12878	blood:	n/a	n/a
44	FOXM1	chr15:75069343-75070417	GM12878	blood:	n/a	n/a
45	EP300	chr15:75069541-75070371	GM12878	blood:	n/a	chr15:75069712-75069728
46	PAX5	chr15:75069599-75070751	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:75069583-75070418	GM15510	blood:	n/a	n/a
48	POLR2A	chr15:75069181-75070589	GM12878	blood:	n/a	n/a
49	ATF2	chr15:75069511-75070290	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:75068884-75070848	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75069513..75071369-chr15:75076004..75078063,2	K562	blood:
2	chr15:75069556..75072054-chr15:75126670..75129004,2	MCF-7	breast:
3	chr15:75067632..75072081-chr15:75073195..75075797,6	MCF-7	breast:
4	chr15:74920881..74923139-chr15:75069434..75070977,2	MCF-7	breast:
5	chr15:75069997..75071811-chr15:75134111..75136567,2	K562	blood:
6	chr15:74923393..74925278-chr15:75068761..75070889,2	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072507	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072508	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591513	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903541	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.89[AMR][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917376	0.94[ASN][1000 genomes]
rs1378940	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378941	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470890	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472304	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.91[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886410	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006567	0.85[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
rs12905199	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12905199	SCAMP5	cis	Artery Tibial	GTEx
rs12905199	SCAMP5	cis	lung	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

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	chr15:75066400-75072400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr15:75066400-75072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:75066600-75072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:75067200-75072800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:75067400-75071000	Enhancers	Brain Hippocampus Middle	brain
12	chr15:75067400-75074200	Enhancers	Stomach Mucosa	stomach
13	chr15:75067600-75070400	Enhancers	Brain Anterior Caudate	brain
14	chr15:75067600-75070400	Enhancers	Brain Cingulate Gyrus	brain
15	chr15:75067600-75071200	Enhancers	Placenta	Placenta
16	chr15:75067600-75071800	Enhancers	Spleen	Spleen
17	chr15:75067600-75071800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr15:75067800-75071800	Enhancers	Small Intestine	intestine
19	chr15:75067800-75072000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:75068000-75073200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:75068600-75070800	Enhancers	Fetal Muscle Leg	muscle
22	chr15:75068600-75071000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr15:75068800-75070400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:75068800-75071200	Enhancers	Esophagus	oesophagus
25	chr15:75068800-75071400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:75068800-75073400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr15:75069000-75070200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:75069000-75070200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:75069000-75070200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:75069000-75070200	Enhancers	Stomach Smooth Muscle	stomach
31	chr15:75069000-75070200	Enhancers	HSMMtube	muscle
32	chr15:75069000-75070400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:75069000-75070400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr15:75069000-75070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:75069000-75070400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:75069000-75070400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr15:75069000-75070400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:75069000-75070400	Enhancers	Right Atrium	heart
39	chr15:75069000-75070600	Enhancers	Brain Substantia Nigra	brain
40	chr15:75069000-75070600	Enhancers	Fetal Stomach	stomach
41	chr15:75069000-75070600	Enhancers	Lung	lung
42	chr15:75069000-75070600	Flanking Active TSS	GM12878-XiMat	blood
43	chr15:75069000-75070600	Flanking Active TSS	HepG2	liver
44	chr15:75069000-75070800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr15:75069000-75070800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:75069000-75070800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:75069000-75070800	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr15:75069000-75070800	Enhancers	HUVEC	blood vessel
49	chr15:75069000-75071200	Enhancers	Fetal Muscle Trunk	muscle
50	chr15:75069000-75072600	Enhancers	Liver	Liver

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