Variant report

Variant	rs7974905
Chromosome Location	chr12:48279413-48279414
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	BCLAF1	chr12:48278621-48279488	GM12878	blood:	n/a	chr12:48278655-48278664
2	NFIC	chr12:48277888-48279460	GM12878	blood:	n/a	n/a
3	CEBPB	chr12:48279407-48279703	K562	blood:	n/a	chr12:48279534-48279545
4	POLR2A	chr12:48278542-48279519	GM12892	blood:	n/a	n/a
5	RELA	chr12:48278312-48279479	GM19193	blood:	n/a	n/a
6	EBF1	chr12:48278678-48279469	GM12878	blood:	n/a	n/a
7	ZEB1	chr12:48278593-48279426	GM12878	blood:	n/a	n/a
8	ATF2	chr12:48278573-48279490	GM12878	blood:	n/a	n/a
9	YY1	chr12:48278798-48279442	GM12878	blood:	n/a	chr12:48279231-48279253
10	PML	chr12:48278499-48279565	GM12878	blood:	n/a	n/a
11	CREB1	chr12:48278298-48279458	GM12878	blood:	n/a	chr12:48278837-48278850
12	RUNX3	chr12:48278255-48279857	GM12878	blood:	n/a	n/a
13	FOXM1	chr12:48278232-48279475	GM12878	blood:	n/a	n/a
14	STAT5A	chr12:48278295-48279795	GM12878	blood:	n/a	chr12:48279059-48279071
15	CEBPB	chr12:48279411-48279700	A549	lung:	n/a	chr12:48279534-48279545
16	RUNX3	chr12:48278253-48279536	GM12878	blood:	n/a	n/a
17	NFATC1	chr12:48278484-48279522	GM12878	blood:	n/a	n/a
18	CEBPB	chr12:48279404-48279708	HepG2	liver:	n/a	chr12:48279534-48279545
19	TBL1XR1	chr12:48278637-48279436	GM12878	blood:	n/a	n/a
20	FOXM1	chr12:48278543-48279474	GM12878	blood:	n/a	n/a
21	CEBPB	chr12:48279370-48279675	K562	blood:	n/a	chr12:48279534-48279545
22	NFATC1	chr12:48278573-48279461	GM12878	blood:	n/a	n/a
23	MTA3	chr12:48275926-48279701	GM12878	blood:	n/a	n/a
24	CEBPB	chr12:48279391-48280078	IMR90	lung:	n/a	chr12:48279534-48279545
25	MEF2A	chr12:48278682-48279415	GM12878	blood:	n/a	n/a
26	BCLAF1	chr12:48278146-48279457	GM12878	blood:	n/a	chr12:48278655-48278664 chr12:48278496-48278505
27	MTA3	chr12:48278713-48279514	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:

Variant related genes	Relation type
VDR	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11574041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2525050	1.00[EUR][1000 genomes]
rs41272781	1.00[EUR][1000 genomes]
rs58436504	1.00[EUR][1000 genomes]
rs61048429	1.00[EUR][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:68 , 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	chr12:48275000-48279800	Enhancers	Fetal Intestine Large	intestine
4	chr12:48275200-48280000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:48275200-48280200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:48275600-48279800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:48275800-48280000	Enhancers	Fetal Thymus	thymus
8	chr12:48276400-48279600	Flanking Active TSS	GM12878-XiMat	blood
9	chr12:48277000-48280200	Enhancers	HMEC	breast
10	chr12:48277000-48286200	Weak transcription	Right Atrium	heart
11	chr12:48277200-48279600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:48277200-48280200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:48277200-48289600	Weak transcription	Esophagus	oesophagus
14	chr12:48277200-48290600	Weak transcription	Gastric	stomach
15	chr12:48277200-48295000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:48277400-48279800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:48277400-48279800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:48277400-48279800	Enhancers	Spleen	Spleen
19	chr12:48277400-48280000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:48277400-48280000	Weak transcription	HSMM	muscle
21	chr12:48277400-48280400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:48277400-48280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:48277400-48282200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:48277600-48279800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr12:48277600-48279800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr12:48277600-48280200	Enhancers	Primary T cells from cord blood	blood
27	chr12:48277600-48280600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:48277600-48281200	Weak transcription	HSMMtube	muscle
29	chr12:48277600-48282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:48277600-48287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:48277600-48289000	Weak transcription	Hela-S3	cervix
32	chr12:48277800-48279600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:48277800-48283000	Weak transcription	Primary B cells from cord blood	blood
34	chr12:48278000-48279600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:48278200-48280400	Enhancers	K562	blood
36	chr12:48278400-48282400	Weak transcription	Small Intestine	intestine
37	chr12:48278400-48282400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:48278400-48283000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:48278400-48287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:48278400-48289600	Weak transcription	Stomach Mucosa	stomach
41	chr12:48278600-48280000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:48278600-48287800	Strong transcription	NHEK	skin
43	chr12:48278800-48279600	Weak transcription	NHDF-Ad	bronchial
44	chr12:48278800-48279800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr12:48278800-48280800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:48278800-48281200	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:48279000-48279800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:48279000-48280400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:48279000-48280800	Enhancers	Osteobl	bone
50	chr12:48279000-48281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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