Variant report

Variant	rs11550108
Chromosome Location	chr12:66563321-66563322
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	SP1	chr12:66562779-66564063	A549	lung:	n/a	chr12:66563015-66563036
2	GTF2F1	chr12:66563144-66563859	H1-hESC	embryonic stem cell:	n/a	n/a
3	YY1	chr12:66562773-66564167	SK-N-SH	brain:	n/a	chr12:66563540-66563548 chr12:66563356-66563370
4	EGR1	chr12:66563180-66564011	MCF-7	breast:	n/a	chr12:66563787-66563796
5	TAL1	chr12:66562910-66563817	K562	blood:	n/a	n/a
6	CCNT2	chr12:66563037-66563953	K562	blood:	n/a	n/a
7	CTCF	chr12:66563290-66563547	A549	lung:	n/a	chr12:66563357-66563370
8	POLR2A	chr12:66562851-66564068	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr12:66562880-66563911	K562	blood:	n/a	n/a
10	HA-E2F1	chr12:66562968-66564353	MCF-7	breast:	n/a	chr12:66563357-66563367 chr12:66563410-66563421
11	YY1	chr12:66563232-66563931	NT2-D1	testis:	n/a	chr12:66563540-66563548 chr12:66563356-66563370
12	POLR2A	chr12:66563026-66564067	A549	lung:	n/a	n/a
13	CTCF	chr12:66563213-66563817	A549	lung:	n/a	chr12:66563357-66563370
14	POLR2A	chr12:66563042-66563917	A549	lung:	n/a	n/a
15	CEBPD	chr12:66562824-66563988	K562	blood:	n/a	chr12:66563083-66563094
16	ZNF217	chr12:66562951-66563897	MCF-7	breast:	n/a	n/a
17	YY1	chr12:66562824-66563952	SK-N-SH_RA	brain:	n/a	chr12:66563540-66563548 chr12:66563356-66563370
18	MYC	chr12:66563241-66563604	K562	blood:	n/a	n/a
19	ELF1	chr12:66563004-66563953	A549	lung:	n/a	chr12:66563560-66563571 chr12:66563561-66563570
20	PAX5	chr12:66563243-66563988	GM12892	blood:	n/a	chr12:66563753-66563772 chr12:66563528-66563538 chr12:66563609-66563628 chr12:66563754-66563772 chr12:66563917-66563926
21	ZKSCAN1	chr12:66562904-66563889	Hela-S3	cervix:	n/a	n/a
22	REST	chr12:66563016-66563564	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr12:66562792-66564070	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr12:66563200-66563350	GM12871	blood:	n/a	n/a
25	POLR2A	chr12:66563049-66563977	HepG2	liver:	n/a	n/a
26	ZBTB7A	chr12:66563275-66563923	K562	blood:	n/a	n/a
27	RXRA	chr12:66563205-66563627	GM12878	blood:	n/a	n/a
28	CHD2	chr12:66562908-66563974	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr12:66563088-66564027	A549	lung:	n/a	n/a
30	EP300	chr12:66562956-66564088	SK-N-SH	brain:	n/a	chr12:66563358-66563367 chr12:66563912-66563926 chr12:66563563-66563570
31	TAF1	chr12:66563007-66563936	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr12:66563069-66563881	GM12878	blood:	n/a	chr12:66563360-66563370
33	CBX3	chr12:66562793-66563966	K562	blood:	n/a	n/a
34	CEBPB	chr12:66562774-66564101	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:66562786-66564029	HUVEC	blood vessel:	n/a	n/a
36	GABPA	chr12:66563303-66563919	HepG2	liver:	n/a	chr12:66563358-66563367
37	POLR2A	chr12:66563014-66563970	HepG2	liver:	n/a	n/a
38	POLR2A	chr12:66562775-66564022	PANC-1	pancreas:	n/a	n/a
39	CTCF	chr12:66563136-66564036	MCF-7	breast:	n/a	chr12:66563357-66563370
40	TCF12	chr12:66563018-66563562	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:66562941-66563971	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:66562857-66563985	HCT-116	colon:	n/a	n/a
43	BRCA1	chr12:66562824-66563957	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr12:66562892-66563350	IMR90	lung:	n/a	n/a
45	REST	chr12:66563016-66564018	K562	blood:	n/a	n/a
46	TAF1	chr12:66562781-66564014	A549	lung:	n/a	n/a
47	HEY1	chr12:66562809-66564000	K562	blood:	n/a	chr12:66563355-66563370
48	ELF1	chr12:66562879-66563962	K562	blood:	n/a	chr12:66563560-66563571 chr12:66563561-66563570
49	YY1	chr12:66563070-66563962	K562	blood:	n/a	chr12:66563540-66563548 chr12:66563356-66563370
50	TBP	chr12:66562782-66563992	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:66563240..66564759-chr12:66582105..66583643,2	MCF-7	breast:
2	chr12:66563193..66563791-chr19:18496498..18497271,2	HCT-116	colon:
3	chr12:66563109..66563876-chr14:50234806..50235310,2	Hela-S3	cervix:
4	chr12:66561525..66563608-chr12:66580703..66583177,2	K562	blood:
5	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
6	chr1:28832139..28832693-chr12:66563217..66564004,2	Hela-S3	cervix:
7	chr12:66562782..66564453-chr5:148959450..148961318,2	MCF-7	breast:
8	chr12:8088335..8089100-chr12:66562765..66563519,2	Hela-S3	cervix:
9	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
10	chr12:66563056..66564656-chr12:66694946..66697705,2	MCF-7	breast:
11	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
12	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:
13	chr12:66563320..66563841-chr3:136557779..136558286,2	MCF-7	breast:
14	chr1:113162099..113162925-chr12:66563110..66563903,2	Hela-S3	cervix:
15	chr12:66562960..66564544-chr12:66668918..66671534,2	MCF-7	breast:
16	chr12:66563062..66563911-chr17:57914982..57915916,2	Hela-S3	cervix:
17	chr12:66562904..66563889-chr8:42948511..42949040,2	Hela-S3	cervix:
18	chr10:88125321..88128301-chr12:66562414..66564569,2	K562	blood:
19	chr12:66563014..66563591-chr9:19379979..19380656,2	HCT-116	colon:
20	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:
21	chr1:11967859..11968598-chr12:66563035..66563806,2	Hela-S3	cervix:

Variant related genes	Relation type
TMBIM4	TF binding region
ENSG00000059804	Chromatin interaction
ENSG00000090376	Chromatin interaction
ENSG00000273486	Chromatin interaction
ENSG00000182771	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000137154	Chromatin interaction
ENSG00000127311	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000256777	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000239335	Chromatin interaction
ENSG00000183111	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000165516	Chromatin interaction
ENSG00000185900	Chromatin interaction
ENSG00000007341	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12099497	1.00[ASN][1000 genomes]
rs34682166	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv899215	chr12:66556960-66594134	Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66561600-66564400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:66562000-66564200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:66562000-66564400	Active TSS	Stomach Smooth Muscle	stomach
4	chr12:66562000-66564400	Active TSS	GM12878-XiMat	blood
5	chr12:66562000-66564400	Active TSS	HSMMtube	muscle
6	chr12:66562200-66564200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:66562200-66564400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:66562200-66564400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:66562200-66564400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:66562200-66564400	Active TSS	NHLF	lung
11	chr12:66562200-66564800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:66562400-66564000	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:66562400-66564200	Active TSS	Right Ventricle	heart
14	chr12:66562400-66564400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:66562400-66564400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:66562400-66564400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:66562400-66564400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:66562400-66564400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:66562400-66564400	Active TSS	Brain Germinal Matrix	brain
20	chr12:66562400-66564400	Active TSS	Colonic Mucosa	Colon
21	chr12:66562400-66564400	Active TSS	HSMM	muscle
22	chr12:66562400-66564400	Active TSS	K562	blood
23	chr12:66562400-66564600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:66562600-66564000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:66562600-66564000	Active TSS	Fetal Thymus	thymus
26	chr12:66562600-66564000	Active TSS	Placenta Amnion	Placenta Amnion
27	chr12:66562600-66564200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:66562600-66564200	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr12:66562600-66564200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:66562600-66564200	Active TSS	Pancreas	Pancrea
31	chr12:66562600-66564200	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr12:66562600-66564200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr12:66562600-66564200	Active TSS	Stomach Mucosa	stomach
34	chr12:66562600-66564200	Active TSS	HMEC	breast
35	chr12:66562600-66564400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:66562600-66564400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:66562600-66564400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:66562600-66564400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:66562600-66564400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:66562600-66564400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:66562600-66564400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:66562600-66564400	Active TSS	Aorta	Aorta
43	chr12:66562600-66564400	Active TSS	Brain Angular Gyrus	brain
44	chr12:66562600-66564400	Active TSS	Brain Anterior Caudate	brain
45	chr12:66562600-66564400	Active TSS	Brain Hippocampus Middle	brain
46	chr12:66562600-66564400	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr12:66562600-66564400	Active TSS	Brain Substantia Nigra	brain
48	chr12:66562600-66564400	Active TSS	Colon Smooth Muscle	Colon
49	chr12:66562600-66564400	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:66562600-66564400	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links