Variant report

Variant	rs7963444
Chromosome Location	chr12:48148180-48148181
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	TCF12	chr12:48146913-48149199	ECC-1	luminal epithelium:	n/a	chr12:48147111-48147121
2	SMC3	chr12:48147227-48148261	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr12:48147967-48148342	T-47D	breast:	n/a	n/a
4	STAT3	chr12:48147929-48148254	MCF10A-Er-Src	breast:	n/a	n/a
5	USF1	chr12:48147110-48148268	ECC-1	luminal epithelium:	n/a	chr12:48147645-48147656
6	TFAP2C	chr12:48146933-48149021	Hela-S3	cervix:	n/a	chr12:48147383-48147398 chr12:48148785-48148800
7	EP300	chr12:48146238-48148408	SK-N-SH	brain:	n/a	chr12:48147400-48147414
8	FOXA1	chr12:48147759-48148352	T-47D	breast:	n/a	n/a
9	MYC	chr12:48147284-48148445	MCF10A-Er-Src	breast:	n/a	chr12:48147647-48147656 chr12:48147645-48147658 chr12:48147647-48147656 chr12:48147646-48147657 chr12:48147645-48147658
10	TEAD4	chr12:48147032-48148306	ECC-1	luminal epithelium:	n/a	n/a
11	TFAP2A	chr12:48147065-48148946	Hela-S3	cervix:	n/a	chr12:48148068-48148079 chr12:48147301-48147316 chr12:48148068-48148079 chr12:48148154-48148169 chr12:48148068-48148079 chr12:48148068-48148079
12	POLR2A	chr12:48146891-48148260	Hela-S3	cervix:	n/a	n/a
13	FOS	chr12:48147516-48148320	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr12:48147169-48148320	MCF10A-Er-Src	breast:	n/a	chr12:48147647-48147656 chr12:48147645-48147658 chr12:48147647-48147656 chr12:48147646-48147657 chr12:48147645-48147658
15	MAX	chr12:48146972-48148245	Hela-S3	cervix:	n/a	chr12:48147647-48147656 chr12:48147645-48147658 chr12:48147647-48147656 chr12:48147646-48147657 chr12:48147645-48147658
16	NFIC	chr12:48146866-48149274	ECC-1	luminal epithelium:	n/a	chr12:48147611-48147639
17	RCOR1	chr12:48147172-48148369	Hela-S3	cervix:	n/a	n/a
18	FOS	chr12:48147689-48148217	MCF10A-Er-Src	breast:	n/a	n/a
19	MAZ	chr12:48147023-48148236	Hela-S3	cervix:	n/a	chr12:48147647-48147656 chr12:48147645-48147658 chr12:48147647-48147656 chr12:48147646-48147657 chr12:48147645-48147658
20	USF2	chr12:48147040-48148270	Hela-S3	cervix:	n/a	chr12:48147645-48147656
21	EP300	chr12:48146839-48150642	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623 chr12:48147400-48147414 chr12:48148703-48148716
22	POLR2A	chr12:48146426-48148248	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr12:48147425-48148242	MCF10A-Er-Src	breast:	n/a	chr12:48147429-48147441 chr12:48147433-48147441
24	SMARCC1	chr12:48146110-48149011	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr12:48146395-48149013	Hela-S3	cervix:	n/a	n/a
26	STAT3	chr12:48148108-48148293	MCF10A-Er-Src	breast:	n/a	n/a
27	TBP	chr12:48147253-48148262	Hela-S3	cervix:	n/a	n/a
28	FOXA1	chr12:48147896-48148295	T-47D	breast:	n/a	n/a
29	CEBPB	chr12:48146893-48148358	Hela-S3	cervix:	n/a	n/a
30	MYC	chr12:48146860-48148518	NB4	blood:	n/a	chr12:48147647-48147656 chr12:48147645-48147658 chr12:48147647-48147656 chr12:48147646-48147657 chr12:48147645-48147658
31	FOS	chr12:48147789-48148254	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48135061..48136993-chr12:48147045..48149552,2	MCF-7	breast:
4	chr12:48147268..48148209-chr12:53342866..53343808,2	Hela-S3	cervix:
5	chr12:48147372..48148186-chr7:123388538..123389440,2	Hela-S3	cervix:
6	chr12:48147317..48148897-chr12:48163637..48165768,2	MCF-7	breast:
7	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:
8	chr12:48147657..48148319-chr3:5020376..5021114,2	Hela-S3	cervix:
9	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
SLC48A1	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000134107	Chromatin interaction
ENSG00000106299	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000272686	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1018939	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875690	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11168224	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168228	0.82[CHD][hapmap]
rs1548518	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs2239189	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7397928	0.89[CHD][hapmap]
rs757286	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757287	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7963444	RAPGEF3	cis	parietal	SCAN
rs7963444	KCNH3	cis	cerebellum	SCAN
rs7963444	VDR	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:48145000-48149000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:48145200-48148600	Genic enhancers	Brain Hippocampus Middle	brain
6	chr12:48145200-48148600	Enhancers	Esophagus	oesophagus
7	chr12:48145200-48149000	Enhancers	HSMM	muscle
8	chr12:48145400-48148400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:48145400-48148400	Genic enhancers	Brain Cingulate Gyrus	brain
10	chr12:48145400-48148800	Enhancers	Left Ventricle	heart
11	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
12	chr12:48145400-48151400	Enhancers	Placenta	Placenta
13	chr12:48145600-48148400	Enhancers	A549	lung
14	chr12:48145600-48149600	Enhancers	Lung	lung
15	chr12:48145600-48149800	Enhancers	HSMMtube	muscle
16	chr12:48145600-48150000	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:48145600-48151000	Enhancers	Spleen	Spleen
20	chr12:48145800-48148200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:48145800-48148200	Enhancers	NHLF	lung
22	chr12:48145800-48148600	Enhancers	Brain Anterior Caudate	brain
23	chr12:48145800-48151200	Enhancers	Gastric	stomach
24	chr12:48146000-48148200	Flanking Active TSS	NHEK	skin
25	chr12:48146000-48149200	Enhancers	Right Atrium	heart
26	chr12:48146000-48149400	Enhancers	Right Ventricle	heart
27	chr12:48146000-48151400	Enhancers	Stomach Mucosa	stomach
28	chr12:48146200-48148800	Enhancers	Osteobl	bone
29	chr12:48146200-48149400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:48146200-48150200	Enhancers	Fetal Muscle Leg	muscle
31	chr12:48146400-48148200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:48146400-48148800	Enhancers	Brain Angular Gyrus	brain
33	chr12:48146600-48148200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:48146600-48148400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:48146600-48148400	Enhancers	NH-A	brain
36	chr12:48146600-48148800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:48146600-48149000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:48146600-48149000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:48146600-48149000	Enhancers	Aorta	Aorta
40	chr12:48146600-48149000	Flanking Active TSS	Hela-S3	cervix
41	chr12:48146600-48149400	Enhancers	Fetal Lung	lung
42	chr12:48146600-48150400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:48146800-48148200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:48146800-48148200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:48146800-48148200	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:48146800-48148800	Flanking Active TSS	HMEC	breast
47	chr12:48147000-48148200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:48147000-48148200	Enhancers	Colon Smooth Muscle	Colon
49	chr12:48147000-48148400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:48147000-48148400	Enhancers	GM12878-XiMat	blood

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