Variant report

Variant	rs11574005
Chromosome Location	chr12:48299570-48299571
allele	A/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	RAD21	chr12:48298197-48299603	SK-N-SH	brain:	n/a	chr12:48298821-48298835
2	MAX	chr12:48297481-48299813	HCT-116	colon:	n/a	chr12:48299521-48299530
3	E2F6	chr12:48298259-48299660	H1-hESC	embryonic stem cell:	n/a	chr12:48298711-48298722 chr12:48298828-48298838 chr12:48298713-48298720 chr12:48299226-48299236 chr12:48298713-48298720 chr12:48298378-48298387 chr12:48298713-48298720
4	MAX	chr12:48298142-48299789	ECC-1	luminal epithelium:	n/a	chr12:48299521-48299530
5	MAX	chr12:48298262-48299695	HCT-116	colon:	n/a	chr12:48299521-48299530
6	GATA3	chr12:48299043-48299620	T-47D	breast:	n/a	n/a
7	CTCF	chr12:48298208-48300165	A549	lung:	n/a	chr12:48299217-48299233
8	CEBPB	chr12:48299214-48299578	K562	blood:	n/a	n/a
9	MAX	chr12:48298264-48299728	ECC-1	luminal epithelium:	n/a	chr12:48299521-48299530
10	EP300	chr12:48298242-48299612	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr12:48298355-48299695	ECC-1	luminal epithelium:	n/a	chr12:48299070-48299077
12	CTCF	chr12:48298273-48299648	SK-N-SH	brain:	n/a	chr12:48299217-48299233
13	MAZ	chr12:48296431-48299667	IMR90	lung:	n/a	chr12:48299521-48299530
14	NFIC	chr12:48298254-48299698	ECC-1	luminal epithelium:	n/a	n/a
15	TBP	chr12:48298389-48299584	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr12:48298299-48299743	IMR90	lung:	n/a	n/a
17	RAD21	chr12:48298267-48299614	HCT-116	colon:	n/a	chr12:48298821-48298835
18	MAX	chr12:48298407-48299578	K562	blood:	n/a	chr12:48299521-48299530
19	MAX	chr12:48298266-48299742	MCF-7	breast:	n/a	chr12:48299521-48299530
20	MAX	chr12:48298247-48299739	A549	lung:	n/a	chr12:48299521-48299530
21	CTCF	chr12:48298856-48299761	HCT-116	colon:	n/a	chr12:48299217-48299233
22	MXI1	chr12:48298258-48299739	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr12:48298236-48299591	ECC-1	luminal epithelium:	n/a	chr12:48298821-48298835
24	GATA3	chr12:48298837-48299683	T-47D	breast:	n/a	n/a
25	CEBPB	chr12:48299010-48299570	IMR90	lung:	n/a	n/a
26	RAD21	chr12:48298872-48299585	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48221119..48223794-chr12:48297710..48299941,2	MCF-7	breast:
2	chr12:48299062..48299693-chr12:48455710..48456429,2	MCF-7	breast:
3	chr12:48275805..48279171-chr12:48299207..48301457,3	K562	blood:
4	chr12:48298691..48299776-chr12:48356759..48358181,8	MCF-7	breast:
5	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:
6	chr12:48298993..48299710-chr12:48357178..48357722,2	MCF-7	breast:
7	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
8	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
9	chr12:48297838..48300182-chr12:48335522..48337383,2	MCF-7	breast:
10	chr12:48211668..48213938-chr12:48298192..48300037,2	MCF-7	breast:
11	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:
12	chr12:48296929..48299891-chr12:48498540..48500341,2	MCF-7	breast:
13	chr12:48298891..48301417-chr12:48363482..48365531,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-3	chr12:48298888-48301381	NONHSAT027959

Variant related genes	Relation type
VDR	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000205537	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000257488	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12721377	1.00[EUR][1000 genomes]
rs7956152	0.93[EUR][1000 genomes]
rs7973209	0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48297000-48299600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48297600-48299600	Active TSS	Small Intestine	intestine
3	chr12:48297600-48299600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr12:48297600-48300000	Active TSS	HSMMtube	muscle
5	chr12:48297800-48299600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr12:48297800-48299600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:48297800-48299600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:48298000-48299600	Active TSS	Esophagus	oesophagus
9	chr12:48298000-48299800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:48298000-48299800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr12:48298000-48300000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:48298200-48299600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:48298200-48299600	Flanking Active TSS	Liver	Liver
14	chr12:48298200-48299600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
15	chr12:48298200-48299600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
16	chr12:48298200-48299600	Active TSS	Pancreas	Pancrea
17	chr12:48298200-48299600	Flanking Active TSS	Right Ventricle	heart
18	chr12:48298200-48299800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr12:48298200-48299800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:48298200-48299800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr12:48298200-48299800	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:48298400-48299600	Bivalent/Poised TSS	Fetal Kidney	kidney
23	chr12:48298400-48299600	Active TSS	Gastric	stomach
24	chr12:48298400-48299600	Active TSS	Hela-S3	cervix
25	chr12:48298400-48299800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:48298400-48299800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:48298600-48299600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr12:48298600-48299600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:48298600-48299600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:48298600-48299600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
31	chr12:48298600-48299600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
32	chr12:48298600-48299600	Active TSS	HepG2	liver
33	chr12:48298600-48299800	Active TSS	Colon Smooth Muscle	Colon
34	chr12:48298600-48300000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:48298600-48300200	Active TSS	Duodenum Mucosa	Duodenum
36	chr12:48298800-48299600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:48298800-48299600	Enhancers	Lung	lung
38	chr12:48299000-48299600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:48299000-48299600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:48299000-48299600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:48299000-48299600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:48299000-48299600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr12:48299000-48299600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
44	chr12:48299000-48299600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr12:48299000-48299600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr12:48299000-48299600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr12:48299000-48299600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:48299000-48299600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr12:48299000-48299600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr12:48299000-48299600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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