Variant report

Variant	rs11168280
Chromosome Location	chr12:48278759-48278760
allele	G/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	BCLAF1	chr12:48278621-48279488	GM12878	blood:	n/a	chr12:48278655-48278664
2	NFIC	chr12:48277888-48279460	GM12878	blood:	n/a	n/a
3	IKZF1	chr12:48278414-48279160	GM12878	blood:	n/a	n/a
4	PAX5	chr12:48278531-48279391	GM12878	blood:	n/a	n/a
5	MEF2C	chr12:48278644-48279387	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:48278542-48279519	GM12892	blood:	n/a	n/a
7	RELA	chr12:48278312-48279479	GM19193	blood:	n/a	n/a
8	EGR1	chr12:48278731-48278969	GM12878	blood:	n/a	chr12:48278847-48278862
9	EBF1	chr12:48278678-48279469	GM12878	blood:	n/a	n/a
10	ZEB1	chr12:48278593-48279426	GM12878	blood:	n/a	n/a
11	EP300	chr12:48278293-48279393	GM12878	blood:	n/a	chr12:48278496-48278510
12	ATF2	chr12:48278573-48279490	GM12878	blood:	n/a	n/a
13	RELA	chr12:48278474-48279384	GM10847	blood:	n/a	n/a
14	CHD2	chr12:48278399-48279299	GM12878	blood:	n/a	n/a
15	PML	chr12:48278499-48279565	GM12878	blood:	n/a	n/a
16	IRF4	chr12:48278146-48279337	GM12878	blood:	n/a	n/a
17	CREB1	chr12:48278298-48279458	GM12878	blood:	n/a	chr12:48278837-48278850
18	IRF4	chr12:48278193-48279220	GM12878	blood:	n/a	n/a
19	RUNX3	chr12:48278255-48279857	GM12878	blood:	n/a	n/a
20	EP300	chr12:48278373-48279273	GM12878	blood:	n/a	chr12:48278496-48278510
21	BATF	chr12:48278650-48279229	GM12878	blood:	n/a	n/a
22	BHLHE40	chr12:48278725-48279331	GM12878	blood:	n/a	n/a
23	FOXM1	chr12:48278232-48279475	GM12878	blood:	n/a	n/a
24	NFIC	chr12:48278162-48279394	GM12878	blood:	n/a	n/a
25	STAT5A	chr12:48278424-48279358	GM12878	blood:	n/a	chr12:48279059-48279071
26	STAT5A	chr12:48278295-48279795	GM12878	blood:	n/a	chr12:48279059-48279071
27	BCL11A	chr12:48278661-48279329	GM12878	blood:	n/a	n/a
28	RUNX3	chr12:48278253-48279536	GM12878	blood:	n/a	n/a
29	NFATC1	chr12:48278484-48279522	GM12878	blood:	n/a	n/a
30	BCL3	chr12:48278654-48279398	GM12878	blood:	n/a	chr12:48278655-48278664
31	POU2F2	chr12:48278674-48279407	GM12891	blood:	n/a	chr12:48278850-48278862
32	ELF1	chr12:48278686-48279313	GM12878	blood:	n/a	n/a
33	TCF12	chr12:48278722-48279390	GM12878	blood:	n/a	chr12:48279272-48279279
34	TBL1XR1	chr12:48278637-48279436	GM12878	blood:	n/a	n/a
35	ATF2	chr12:48278625-48279288	GM12878	blood:	n/a	n/a
36	SP1	chr12:48278622-48279330	GM12878	blood:	n/a	chr12:48278846-48278856 chr12:48278987-48278999 chr12:48278987-48278999 chr12:48278637-48278646
37	FOXM1	chr12:48278543-48279474	GM12878	blood:	n/a	n/a
38	CEBPB	chr12:48278591-48279393	GM12878	blood:	n/a	n/a
39	SP1	chr12:48278676-48279292	GM12878	blood:	n/a	chr12:48278846-48278856 chr12:48278987-48278999 chr12:48278987-48278999
40	MEF2A	chr12:48278661-48279356	GM12878	blood:	n/a	n/a
41	EGR1	chr12:48278730-48279275	GM12878	blood:	n/a	chr12:48278984-48278998 chr12:48278847-48278862
42	NFATC1	chr12:48278573-48279461	GM12878	blood:	n/a	n/a
43	EP300	chr12:48278728-48279159	GM12878	blood:	n/a	n/a
44	TCF12	chr12:48278662-48279348	GM12878	blood:	n/a	chr12:48279272-48279279
45	EP300	chr12:48278661-48279207	GM12878	blood:	n/a	n/a
46	MTA3	chr12:48275926-48279701	GM12878	blood:	n/a	n/a
47	RCOR1	chr12:48278386-48279336	GM12878	blood:	n/a	n/a
48	BATF	chr12:48278117-48279339	GM12878	blood:	n/a	n/a
49	TCF3	chr12:48278601-48279386	GM12878	blood:	n/a	n/a
50	MEF2A	chr12:48278682-48279415	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48276795..48279456-chr12:48285534..48287746,2	MCF-7	breast:
2	chr12:48276120..48279378-chr12:48295337..48299363,4	MCF-7	breast:

Variant related genes	Relation type
VDR	TF binding region
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10160938	1.00[AMR][1000 genomes]
rs11168352	1.00[AMR][1000 genomes]
rs12300777	1.00[AMR][1000 genomes]
rs12308796	1.00[AMR][1000 genomes]
rs12317373	1.00[AMR][1000 genomes]
rs74085274	0.97[AFR][1000 genomes];1.00[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	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
2	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

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48265000-48283200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:48273800-48278800	Enhancers	NHDF-Ad	bronchial
4	chr12:48275000-48279800	Enhancers	Fetal Intestine Large	intestine
5	chr12:48275200-48279200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48275200-48280000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48275200-48280200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:48275600-48279800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:48275800-48280000	Enhancers	Fetal Thymus	thymus
10	chr12:48276400-48279600	Flanking Active TSS	GM12878-XiMat	blood
11	chr12:48277000-48278800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48277000-48280200	Enhancers	HMEC	breast
13	chr12:48277000-48286200	Weak transcription	Right Atrium	heart
14	chr12:48277200-48279000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:48277200-48279200	Enhancers	Colonic Mucosa	Colon
16	chr12:48277200-48279400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:48277200-48279400	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:48277200-48279600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:48277200-48280200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:48277200-48289600	Weak transcription	Esophagus	oesophagus
21	chr12:48277200-48290600	Weak transcription	Gastric	stomach
22	chr12:48277200-48295000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:48277400-48278800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:48277400-48279000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:48277400-48279000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:48277400-48279400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:48277400-48279400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:48277400-48279800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:48277400-48279800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:48277400-48279800	Enhancers	Spleen	Spleen
31	chr12:48277400-48280000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:48277400-48280000	Weak transcription	HSMM	muscle
33	chr12:48277400-48280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:48277400-48280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:48277400-48282200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:48277600-48278800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:48277600-48278800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:48277600-48278800	Weak transcription	Lung	lung
39	chr12:48277600-48279000	Weak transcription	Osteobl	bone
40	chr12:48277600-48279400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:48277600-48279400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:48277600-48279800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:48277600-48279800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:48277600-48280200	Enhancers	Primary T cells from cord blood	blood
45	chr12:48277600-48280600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr12:48277600-48281200	Weak transcription	HSMMtube	muscle
47	chr12:48277600-48282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:48277600-48287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:48277600-48289000	Weak transcription	Hela-S3	cervix
50	chr12:48277800-48278800	Weak transcription	Primary hematopoietic stem cells	blood

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