Variant report

Variant	rs1548518
Chromosome Location	chr12:48152995-48152996
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	CTCF	chr12:48152900-48153050	GM12874	blood:	n/a	n/a
2	ETS1	chr12:48152629-48153119	A549	lung:	n/a	chr12:48152734-48152745
3	MAX	chr12:48152386-48153668	HCT-116	colon:	n/a	chr12:48152950-48152963 chr12:48152952-48152961 chr12:48152951-48152962 chr12:48152734-48152744 chr12:48152952-48152962 chr12:48152952-48152962
4	SMARCB1	chr12:48152398-48153645	Hela-S3	cervix:	n/a	chr12:48153007-48153016
5	USF1	chr12:48152724-48153103	A549	lung:	n/a	chr12:48152951-48152962
6	USF1	chr12:48152713-48153156	A549	lung:	n/a	chr12:48153097-48153113 chr12:48152951-48152962
7	ESR1	chr12:48152648-48153099	ECC-1	luminal epithelium:	n/a	n/a
8	FOXA1	chr12:48152644-48153260	HepG2	liver:	n/a	n/a
9	FOSL1	chr12:48152802-48153187	K562	blood:	n/a	chr12:48153007-48153016 chr12:48152930-48152938 chr12:48153006-48153017
10	POLR2A	chr12:48151449-48153264	NB4	blood:	n/a	n/a
11	SMC3	chr12:48152583-48153497	Hela-S3	cervix:	n/a	chr12:48152864-48152874 chr12:48153189-48153199 chr12:48153359-48153366 chr12:48153352-48153366
12	POLR2A	chr12:48152575-48153463	SK-N-MC	brain:	n/a	n/a
13	USF1	chr12:48152623-48153172	SK-N-SH	brain:	n/a	chr12:48153097-48153113 chr12:48152951-48152962
14	FOXM1	chr12:48151523-48153764	ECC-1	luminal epithelium:	n/a	n/a
15	ZNF143	chr12:48152778-48153499	K562	blood:	n/a	n/a
16	CTCF	chr12:48152806-48153096	GM12891	blood:	n/a	n/a
17	UBTF	chr12:48152833-48153485	K562	blood:	n/a	n/a
18	POLR2A	chr12:48152645-48153494	K562	blood:	n/a	n/a
19	CTCF	chr12:48152900-48153050	GM12875	blood:	n/a	n/a
20	USF1	chr12:48152800-48153067	GM12878	blood:	n/a	chr12:48152951-48152962
21	MAFK	chr12:48152946-48153029	K562	blood:	n/a	n/a
22	CTCF	chr12:48152543-48153543	H1-hESC	embryonic stem cell:	n/a	chr12:48153350-48153368 chr12:48153353-48153363 chr12:48153189-48153202
23	MAX	chr12:48152326-48153584	MCF-7	breast:	n/a	chr12:48152950-48152963 chr12:48152952-48152961 chr12:48152951-48152962 chr12:48152734-48152744 chr12:48152952-48152962 chr12:48152952-48152962
24	USF2	chr12:48152776-48153134	Hela-S3	cervix:	n/a	chr12:48153097-48153113 chr12:48152951-48152962
25	CTCF	chr12:48152860-48153010	HMF	breast:	n/a	n/a
26	POLR2A	chr12:48152442-48153224	U87	brain:	n/a	n/a
27	FOXA1	chr12:48152727-48153108	ECC-1	luminal epithelium:	n/a	n/a
28	TBP	chr12:48152820-48153267	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr12:48152931-48153051	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:48152493-48153783	HCT-116	colon:	n/a	chr12:48153350-48153368 chr12:48153353-48153363 chr12:48153189-48153202
31	ESR1	chr12:48152531-48153418	ECC-1	luminal epithelium:	n/a	n/a
32	USF1	chr12:48152723-48153127	H1-hESC	embryonic stem cell:	n/a	chr12:48153097-48153113 chr12:48152951-48152962
33	STAT3	chr12:48152885-48153139	MCF10A-Er-Src	breast:	n/a	chr12:48153000-48153012 chr12:48153054-48153065
34	SIN3AK20	chr12:48152749-48153113	H1-hESC	embryonic stem cell:	n/a	n/a
35	HEY1	chr12:48152667-48153396	K562	blood:	n/a	n/a
36	CTCF	chr12:48152709-48153571	GM12878	blood:	n/a	chr12:48153350-48153368 chr12:48153353-48153363 chr12:48153189-48153202
37	POLR2A	chr12:48152299-48153408	U87	brain:	n/a	n/a
38	E2F6	chr12:48152432-48153205	A549	lung:	n/a	chr12:48153128-48153135 chr12:48153128-48153135 chr12:48152703-48152712 chr12:48152736-48152745 chr12:48153128-48153135 chr12:48153099-48153109
39	CTCF	chr12:48152880-48153030	HCT-116	colon:	n/a	n/a
40	CTCF	chr12:48152888-48153005	LNCaP	prostate:	n/a	n/a
41	MYC	chr12:48152735-48153432	K562	blood:	n/a	chr12:48152950-48152963 chr12:48152952-48152961 chr12:48152951-48152962 chr12:48152952-48152962 chr12:48152952-48152962
42	FOS	chr12:48152815-48153190	MCF10A-Er-Src	breast:	n/a	chr12:48153007-48153016 chr12:48152930-48152938 chr12:48153006-48153017
43	MAZ	chr12:48152600-48153483	GM12878	blood:	n/a	chr12:48152950-48152963 chr12:48152952-48152961 chr12:48152951-48152962 chr12:48152734-48152744 chr12:48152952-48152962 chr12:48152952-48152962
44	NR2F2	chr12:48152657-48153469	K562	blood:	n/a	n/a
45	RAD21	chr12:48152812-48153365	H1-hESC	embryonic stem cell:	n/a	chr12:48153189-48153199 chr12:48152864-48152874 chr12:48153187-48153199 chr12:48152862-48152875
46	POLR2A	chr12:48152738-48153111	GM12878	blood:	n/a	n/a
47	CTCF	chr12:48152849-48153049	MCF-7	breast:	n/a	n/a
48	JUND	chr12:48152831-48153104	H1-hESC	embryonic stem cell:	n/a	chr12:48153007-48153016 chr12:48152930-48152938 chr12:48153006-48153017
49	POLR2A	chr12:48152469-48153479	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr12:48152880-48153030	AoAF	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48152951-48153001	HepG2	liver:	n/a
2	chr12:48152951-48153001	T-47D	breast:	n/a
3	chr12:48152951-48153001	AG10803	skin:	n/a
4	chr12:48152951-48153001	Caco-2	colon:	n/a
5	chr12:48152951-48153001	HRE	kidney:	n/a
6	chr12:48152951-48153001	AG04449	skin:	fetal
7	chr12:48152951-48153001	HPAEpiC	pulmonary alveolar:	n/a
8	chr12:48152951-48153001	HRPEpiC	eye:	n/a
9	chr12:48152951-48153001	H1-hESC	embryonic stem cell:	embryo
10	chr12:48152951-48153001	NB4	blood:	n/a
11	chr12:48152951-48153001	RPTEC	kidney:	n/a
12	chr12:48152951-48153001	AG09309	skin:	n/a
13	chr12:48152951-48153001	GM12891	blood:	n/a
14	chr12:48152951-48153001	NT2-D1	testis:	n/a
15	chr12:48152951-48153001	HUVEC	blood vessel:	n/a
16	chr12:48152951-48153001	HEK293	kidney:	embryo
17	chr12:48152951-48153001	NHDF-neo	bronchial:	n/a
18	chr12:48152951-48153001	LNCaP	prostate:	n/a
19	chr12:48152951-48153001	ProgFib	skin:	n/a
20	chr12:48152951-48153001	HIPEpiC	eye:	n/a
21	chr12:48152951-48153001	AG09319	gingival:	n/a
22	chr12:48152951-48153001	AoSMC	blood vessel:	n/a
23	chr12:48152951-48153001	ECC-1	luminal epithelium:	n/a
24	chr12:48152951-48153001	HRCEpiC	kidney:	n/a
25	chr12:48152951-48153001	A549	lung:	n/a
26	chr12:48152951-48153001	PANC-1	pancreas:	n/a
27	chr12:48152951-48153001	HAEpiC	amniotic membrane:	n/a
28	chr12:48152951-48153001	HCPEpiC	choroid plexus:	n/a
29	chr12:48152951-48153001	SKMC	muscle:	n/a
30	chr12:48152951-48153001	NH-A	brain:	n/a
31	chr12:48152951-48153001	GM12892	blood:	n/a
32	chr12:48152951-48153001	BJ	skin:	n/a
33	chr12:48152951-48153001	Hepatocyte	liver:	n/a
34	chr12:48152951-48153001	Hela-S3	cervix:	n/a
35	chr12:48152951-48153001	HEEpiC	esophagus:	n/a
36	chr12:48152951-48153001	CMK	blood:	n/a
37	chr12:48152951-48153001	GM12878	blood:	n/a
38	chr12:48152951-48153001	Jurkat	blood:	n/a
39	chr12:48152951-48153001	SK-N-SH_RA	brain:	n/a
40	chr12:48152951-48153001	HCT-116	colon:	n/a
41	chr12:48152951-48153001	HCF	heart:	n/a
42	chr12:48152951-48153001	HL-60	blood:	n/a
43	chr12:48152951-48153001	BE2_C	brain:	n/a
44	chr12:48152951-48153001	SK-N-SH	brain:	n/a
45	chr12:48152951-48153001	ovcar-3	ovarian:	n/a
46	chr12:48152951-48153001	GM19239	blood:	n/a
47	chr12:48152951-48153001	AG04450	lung:	fetal
48	chr12:48152951-48153001	PFSK-1	brain:	n/a
49	chr12:48152951-48153001	NHBE	bronchial:	n/a
50	chr12:48152951-48153001	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48151756..48154631-chr12:48166805..48168592,3	MCF-7	breast:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48137493..48138878-chr12:48152464..48153861,18	MCF-7	breast:
4	chr12:48151483..48157972-chr12:48164331..48169743,9	K562	blood:
5	chr12:48099022..48099877-chr12:48152859..48153391,2	MCF-7	breast:
6	chr12:48151782..48154257-chr12:48166848..48168699,2	MCF-7	breast:
7	chr12:48135721..48136674-chr12:48152904..48153797,3	K562	blood:
8	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
9	chr12:48135732..48136292-chr12:48152879..48153484,2	MCF-7	breast:
10	chr12:48097907..48100262-chr12:48151350..48154397,3	K562	blood:
11	chr12:48135691..48136363-chr12:48152705..48153606,3	MCF-7	breast:
12	chr12:48152241..48154431-chr12:48164400..48166889,3	K562	blood:

Variant related genes	Relation type
RAPGEF3	TF binding region
RAPGEF3	CpG island
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10875690	0.84[CHD][hapmap]
rs11168224	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs2239189	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7397928	0.84[CHD][hapmap]
rs7963444	0.86[CHB][hapmap];0.95[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic 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	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv518315	chr12:48149752-48152995	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1548518	PUS7L	cis	parietal	SCAN
rs1548518	HDAC7	cis	cerebellum	SCAN
rs1548518	RAPGEF3	cis	cerebellum	SCAN
rs1548518	TMEM117	cis	cerebellum	SCAN
rs1548518	RAPGEF3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48149000-48153800	Active TSS	Psoas Muscle	Psoas
2	chr12:48149800-48153200	Active TSS	Left Ventricle	heart
3	chr12:48149800-48153600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:48151000-48153200	Active TSS	Lung	lung
5	chr12:48151000-48153600	Flanking Active TSS	Fetal Muscle Leg	muscle
6	chr12:48151000-48154200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:48151200-48153200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:48151200-48153600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:48151200-48153600	Enhancers	Fetal Brain Male	brain
10	chr12:48151200-48153800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:48151400-48153400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:48151400-48153400	Active TSS	Fetal Kidney	kidney
13	chr12:48151400-48153600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr12:48151400-48153600	Flanking Active TSS	Placenta	Placenta
15	chr12:48151400-48153600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr12:48151400-48153600	Flanking Active TSS	HMEC	breast
17	chr12:48151600-48153400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:48151600-48153400	Active TSS	Brain Angular Gyrus	brain
19	chr12:48151600-48153800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr12:48151800-48153200	Active TSS	Right Atrium	heart
21	chr12:48151800-48153400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:48151800-48153400	Active TSS	Brain Hippocampus Middle	brain
23	chr12:48151800-48153800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr12:48152000-48153000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:48152000-48153200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:48152000-48153200	Active TSS	Brain Substantia Nigra	brain
27	chr12:48152000-48153200	Active TSS	Ovary	ovary
28	chr12:48152000-48153400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:48152000-48153400	Flanking Active TSS	Thymus	Thymus
30	chr12:48152200-48153200	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:48152200-48153200	Active TSS	Brain Cingulate Gyrus	brain
32	chr12:48152200-48153400	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr12:48152200-48153400	Active TSS	Aorta	Aorta
34	chr12:48152200-48153600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:48152200-48153600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:48152200-48153600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr12:48152200-48153600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr12:48152200-48153600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr12:48152200-48153600	Flanking Bivalent TSS/Enh	Dnd41	blood
40	chr12:48152200-48153800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr12:48152400-48153000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:48152400-48153000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:48152400-48153000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:48152400-48153000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:48152400-48153200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:48152400-48153200	Active TSS	Primary T cells from cord blood	blood
47	chr12:48152400-48153200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr12:48152400-48153400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48152400-48153400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:48152400-48153400	Active TSS	Gastric	stomach

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