Variant report

Variant	rs12912343
Chromosome Location	chr15:75251041-75251042
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr15:75250711-75251094	HEK293-T-REx	kidney:	n/a	chr15:75250902-75250911 chr15:75250897-75250918
2	CTCF	chr15:75250940-75251090	RPTEC	kidney:	n/a	n/a
3	CTCF	chr15:75250960-75251110	HMF	breast:	n/a	n/a
4	CTCF	chr15:75250980-75251130	A549	lung:	n/a	chr15:75251113-75251122
5	SIN3AK20	chr15:75250423-75251765	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr15:75250583-75251198	A549	lung:	n/a	n/a
7	CTCF	chr15:75250914-75251085	Pancreas_OC	pancreas:	n/a	n/a
8	POLR2A	chr15:75250534-75251137	HCT-116	colon:	n/a	n/a
9	ELF1	chr15:75250796-75251219	HepG2	liver:	n/a	chr15:75250972-75250985 chr15:75250805-75250817
10	CTCF	chr15:75250900-75251050	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr15:75247844-75251217	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:75250680-75251246	HepG2	liver:	n/a	n/a
13	CTCF	chr15:75250940-75251090	HepG2	liver:	n/a	n/a
14	ELF1	chr15:75250823-75251265	HepG2	liver:	n/a	chr15:75250972-75250985
15	POLR2A	chr15:75250642-75251159	SK-N-MC	brain:	n/a	n/a
16	CTCF	chr15:75250920-75251070	HRE	kidney:	n/a	n/a
17	CTCF	chr15:75250900-75251050	HCFaa	heart:	n/a	n/a
18	CTCF	chr15:75250920-75251070	BJ	skin:	n/a	n/a
19	CTCF	chr15:75250920-75251070	MCF-7	breast:	n/a	n/a
20	CTCF	chr15:75250900-75251050	BE2_C	brain:	n/a	n/a
21	POLR2A	chr15:75250445-75251152	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr15:75250391-75251417	A549	lung:	n/a	n/a
23	CTCF	chr15:75250920-75251070	HPAF	blood vessel:	n/a	n/a
24	CTCF	chr15:75250996-75251045	Fibrobl	skin:	n/a	n/a
25	ELF1	chr15:75250635-75251402	MCF-7	breast:	n/a	chr15:75250972-75250985 chr15:75250805-75250817
26	CTCF	chr15:75248287-75251407	A549	lung:	n/a	chr15:75251113-75251122
27	ELK1	chr15:75250919-75251114	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr15:75250960-75251110	HUVEC	blood vessel:	n/a	n/a
29	HNF4G	chr15:75250857-75251342	HepG2	liver:	n/a	chr15:75251067-75251082
30	POLR2A	chr15:75250631-75251136	A549	lung:	n/a	n/a
31	RUNX3	chr15:75250850-75251188	GM12878	blood:	n/a	n/a
32	CTCF	chr15:75250920-75251070	NHDF-neo	bronchial:	n/a	n/a
33	HEY1	chr15:75250806-75251244	HepG2	liver:	n/a	n/a
34	CTCF	chr15:75250940-75251090	HPAF	blood vessel:	n/a	n/a
35	CTCF	chr15:75250980-75251130	NHDF-neo	bronchial:	n/a	chr15:75251113-75251122
36	MAZ	chr15:75250731-75251087	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr15:75250960-75251110	HRPEpiC	eye:	n/a	n/a
38	GABPA	chr15:75250748-75251198	A549	lung:	n/a	n/a
39	POLR2A	chr15:75250521-75251163	U87	brain:	n/a	n/a
40	CTCF	chr15:75251000-75251150	GM12873	blood:	n/a	chr15:75251113-75251122
41	CTCF	chr15:75250901-75251179	H1-hESC	embryonic stem cell:	n/a	chr15:75251113-75251122
42	CTCF	chr15:75250940-75251090	SAEC	small airway:	n/a	n/a
43	CTCF	chr15:75250920-75251070	AoAF	blood vessel:	n/a	n/a
44	CTCF	chr15:75250920-75251070	AG09319	gingival:	n/a	n/a
45	CTCF	chr15:75250900-75251050	HBMEC	blood vessel:	n/a	n/a
46	POLR2A	chr15:75250584-75251157	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr15:75250855-75251067	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:75250335-75251231	U87	brain:	n/a	n/a
49	POLR2A	chr15:75250462-75251429	PANC-1	pancreas:	n/a	n/a
50	CTCF	chr15:75250900-75251050	HMEC	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:75250997-75251047	HRPEpiC	eye:	n/a
2	chr15:75250997-75251047	NHBE	bronchial:	n/a
3	chr15:75250997-75251047	K562	blood:	n/a
4	chr15:75250997-75251047	HEK293	kidney:	embryo
5	chr15:75250997-75251047	ECC-1	luminal epithelium:	n/a
6	chr15:75250997-75251047	ProgFib	skin:	n/a
7	chr15:75250997-75251047	HepG2	liver:	n/a
8	chr15:75250997-75251047	ovcar-3	ovarian:	n/a
9	chr15:75250997-75251047	GM12878	blood:	n/a
10	chr15:75250997-75251047	HRE	kidney:	n/a
11	chr15:75250997-75251047	NHDF-neo	bronchial:	n/a
12	chr15:75250997-75251047	HCPEpiC	choroid plexus:	n/a
13	chr15:75250997-75251047	AoSMC	blood vessel:	n/a
14	chr15:75250997-75251047	NH-A	brain:	n/a
15	chr15:75250997-75251047	AG09309	skin:	n/a
16	chr15:75250997-75251047	HUVEC	blood vessel:	n/a
17	chr15:75250997-75251047	LNCaP	prostate:	n/a
18	chr15:75250997-75251047	AG04450	lung:	fetal
19	chr15:75250997-75251047	AG04449	skin:	fetal
20	chr15:75250997-75251047	PrEC	prostate:	n/a
21	chr15:75250997-75251047	GM12891	blood:	n/a
22	chr15:75250997-75251047	HIPEpiC	eye:	n/a
23	chr15:75250997-75251047	Caco-2	colon:	n/a
24	chr15:75250997-75251047	MCF-7	breast:	n/a
25	chr15:75250997-75251047	BJ	skin:	n/a
26	chr15:75250997-75251047	HPAEpiC	pulmonary alveolar:	n/a
27	chr15:75250997-75251047	PANC-1	pancreas:	n/a
28	chr15:75250997-75251047	BE2_C	brain:	n/a
29	chr15:75250997-75251047	HNPCEpiC	eye:	n/a
30	chr15:75250997-75251047	Jurkat	blood:	n/a
31	chr15:75250997-75251047	SKMC	muscle:	n/a
32	chr15:75250997-75251047	RPTEC	kidney:	n/a
33	chr15:75250997-75251047	GM12892	blood:	n/a
34	chr15:75250997-75251047	Hepatocyte	liver:	n/a
35	chr15:75250997-75251047	SAEC	small airway:	n/a
36	chr15:75250997-75251047	HMEC	breast:	n/a
37	chr15:75250997-75251047	U87	brain:	n/a
38	chr15:75250997-75251047	A549	lung:	n/a
39	chr15:75250997-75251047	AG09319	gingival:	n/a
40	chr15:75250997-75251047	PFSK-1	brain:	n/a
41	chr15:75250997-75251047	NB4	blood:	n/a
42	chr15:75250997-75251047	H1-hESC	embryonic stem cell:	embryo
43	chr15:75250997-75251047	SK-N-MC	brain:	n/a
44	chr15:75250997-75251047	MCF10A-Er-Src	breast:	n/a
45	chr15:75250997-75251047	SK-N-SH_RA	brain:	n/a
46	chr15:75250997-75251047	HCT-116	colon:	n/a
47	chr15:75250997-75251047	HAEpiC	amniotic membrane:	n/a
48	chr15:75250997-75251047	NT2-D1	testis:	n/a
49	chr15:75250997-75251047	T-47D	breast:	n/a
50	chr15:75250997-75251047	GM06990	blood:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75250034..75252437-chr15:75257925..75259887,2	K562	blood:
2	chr15:75226056..75232063-chr15:75248745..75252832,9	MCF-7	breast:
3	chr15:75248197..75251380-chr15:75494107..75498676,4	MCF-7	breast:
4	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
5	chr15:75249528..75251223-chr15:75287946..75289828,2	K562	blood:
6	chr15:75181382..75185367-chr15:75245501..75252189,8	K562	blood:
7	chr15:75129762..75131472-chr15:75249225..75252165,2	K562	blood:
8	chr15:75134593..75136676-chr15:75247766..75251919,4	MCF-7	breast:
9	chr15:75250875..75251506-chr3:149375277..149375820,2	Hela-S3	cervix:
10	chr15:75249199..75251809-chr15:75494359..75496397,2	K562	blood:
11	chr15:75250701..75253480-chr15:75254260..75256998,2	K562	blood:
12	chr15:75250762..75251638-chr22:50246556..50247418,2	Hela-S3	cervix:
13	chr15:75194037..75196796-chr15:75249908..75252544,2	K562	blood:
14	chr15:75247469..75252493-chr15:75314645..75318771,7	MCF-7	breast:

No data

Variant related genes	Relation type
RPP25	TF binding region
RPP25	CpG island
ENSG00000140474	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000018408	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072514	0.83[AMR][1000 genomes]
rs1133323	0.81[AMR][1000 genomes]
rs11630087	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630592	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11636892	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639413	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856413	0.81[AMR][1000 genomes]
rs12901190	0.85[AMR][1000 genomes]
rs12903370	0.83[AMR][1000 genomes]
rs12904326	0.81[AMR][1000 genomes]
rs12909335	0.81[AMR][1000 genomes]
rs12912839	0.81[AMR][1000 genomes]
rs2044157	0.85[AMR][1000 genomes]
rs2415251	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34063670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34307821	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34799293	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35556055	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35882241	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886413	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338926	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62029217	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.81[AMR][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12912343	SCAMP2	cis	Whole Blood	GTEx
rs12912343	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12912343	SCAMP5	cis	lung	GTEx
rs12912343	SCAMP5	cis	Artery Tibial	GTEx
rs12912343	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12912343	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75246800-75251800	Flanking Active TSS	HUVEC	blood vessel
2	chr15:75247400-75251600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr15:75247600-75252000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr15:75247800-75251800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:75247800-75252400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:75248200-75252200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr15:75248200-75252200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr15:75248200-75252400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:75248400-75251800	Active TSS	Aorta	Aorta
10	chr15:75248400-75251800	Active TSS	NHDF-Ad	bronchial
11	chr15:75249200-75251200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr15:75249200-75251400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:75249400-75251200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:75249400-75251200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr15:75249400-75251400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:75249400-75251600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
17	chr15:75249400-75251800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
18	chr15:75249400-75251800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
19	chr15:75249400-75251800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
20	chr15:75249400-75252200	Bivalent Enhancer	Fetal Brain Male	brain
21	chr15:75249600-75251600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:75249600-75251600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:75249600-75252000	Bivalent Enhancer	Primary B cells from cord blood	blood
24	chr15:75249600-75252200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:75249600-75252200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:75249800-75251200	Bivalent/Poised TSS	NHLF	lung
27	chr15:75249800-75251600	Flanking Bivalent TSS/Enh	Placenta	Placenta
28	chr15:75249800-75251800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:75249800-75252000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:75249800-75252000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:75250000-75251200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:75250000-75251200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr15:75250000-75251400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:75250000-75251600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:75250000-75251600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:75250000-75251600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr15:75250000-75251600	Bivalent Enhancer	Fetal Thymus	thymus
38	chr15:75250000-75251600	Active TSS	Gastric	stomach
39	chr15:75250000-75251600	Bivalent/Poised TSS	Thymus	Thymus
40	chr15:75250000-75251800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
41	chr15:75250000-75251800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr15:75250000-75251800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr15:75250000-75251800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr15:75250000-75252000	Bivalent/Poised TSS	Fetal Brain Female	brain
45	chr15:75250000-75252200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr15:75250000-75252200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr15:75250200-75251200	Bivalent/Poised TSS	HepG2	liver
48	chr15:75250200-75251400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:75250200-75251800	Bivalent Enhancer	Fetal Heart	heart
50	chr15:75250200-75251800	Bivalent/Poised TSS	Osteobl	bone

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