Variant report

Variant	esv3423758
Chromosome Location	chr12:106646369-106649583
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr12:106648488-106648849	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr12:106646453-106646644	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr12:106646358-106646710	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:106646362-106646708	IMR90	lung:	n/a	n/a
5	CEBPB	chr12:106646528-106646612	K562	blood:	n/a	n/a
6	CEBPB	chr12:106646357-106646699	A549	lung:	n/a	n/a
7	ESR1	chr12:106648495-106648832	ECC-1	luminal epithelium:	n/a	n/a
8	ESR1	chr12:106648427-106648882	ECC-1	luminal epithelium:	n/a	n/a
9	ESR1	chr12:106648425-106648909	ECC-1	luminal epithelium:	n/a	n/a
10	ESR1	chr12:106648469-106648951	ECC-1	luminal epithelium:	n/a	n/a
11	ESR1	chr12:106648440-106648859	ECC-1	luminal epithelium:	n/a	n/a
12	GTF2F1	chr12:106648516-106648696	H1-hESC	embryonic stem cell:	n/a	n/a
13	IRF1	chr12:106646805-106646811	K562	blood:	n/a	n/a
14	JUN	chr12:106648523-106649113	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr12:106648395-106648898	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUND	chr12:106649420-106649436	H1-hESC	embryonic stem cell:	n/a	n/a
17	KAP1	chr12:106648416-106648925	U2OS	brain:	n/a	n/a
18	MAX	chr12:106648596-106648899	H1-hESC	embryonic stem cell:	n/a	n/a
19	NFIC	chr12:106648371-106648940	ECC-1	luminal epithelium:	n/a	n/a
20	NFIC	chr12:106648459-106649080	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr12:106647323-106648358	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:106648062-106648259	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr12:106648564-106648704	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr12:106646615-106646825	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:106646536-106646733	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:106648643-106648790	MCF10A-Er-Src	breast:	n/a	n/a
27	SP1	chr12:106648414-106648860	H1-hESC	embryonic stem cell:	n/a	n/a
28	TCF7L2	chr12:106648226-106648925	HEK293	kidney:	n/a	n/a
29	TCF7L2	chr12:106648529-106648945	HCT-116	colon:	n/a	n/a
30	TCF7L2	chr12:106648646-106648906	Hela-S3	cervix:	n/a	n/a
31	YY1	chr12:106648457-106649021	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:106648541-106648591	AG09319	gingival:	n/a
2	chr12:106648541-106648591	T-47D	breast:	n/a
3	chr12:106648541-106648591	MCF10A-Er-Src	breast:	n/a
4	chr12:106648541-106648591	HRCEpiC	kidney:	n/a
5	chr12:106648541-106648591	CMK	blood:	n/a
6	chr12:106648541-106648591	HPAEpiC	pulmonary alveolar:	n/a
7	chr12:106648541-106648591	HCF	heart:	n/a
8	chr12:106648541-106648591	SK-N-MC	brain:	n/a
9	chr12:106648541-106648591	HRPEpiC	eye:	n/a
10	chr12:106648541-106648591	SK-N-SH_RA	brain:	n/a
11	chr12:106648541-106648591	GM12891	blood:	n/a
12	chr12:106648541-106648591	IMR90	lung:	fetal
13	chr12:106648541-106648591	K562	blood:	n/a
14	chr12:106648541-106648591	SK-N-SH	brain:	n/a
15	chr12:106648541-106648591	HRE	kidney:	n/a
16	chr12:106648541-106648591	HUVEC	blood vessel:	n/a
17	chr12:106648541-106648591	HNPCEpiC	eye:	n/a
18	chr12:106648541-106648591	A549	lung:	n/a
19	chr12:106648541-106648591	PFSK-1	brain:	n/a
20	chr12:106648541-106648591	HCT-116	colon:	n/a
21	chr12:106648541-106648591	HCPEpiC	choroid plexus:	n/a
22	chr12:106648541-106648591	GM19239	blood:	n/a
23	chr12:106648541-106648591	HIPEpiC	eye:	n/a
24	chr12:106648541-106648591	HEEpiC	esophagus:	n/a
25	chr12:106648541-106648591	MCF-7	breast:	n/a
26	chr12:106648541-106648591	NHDF-neo	bronchial:	n/a
27	chr12:106648541-106648591	NHBE	bronchial:	n/a
28	chr12:106648541-106648591	HCM	heart:	n/a
29	chr12:106648541-106648591	Hepatocyte	liver:	n/a
30	chr12:106648541-106648591	PrEC	prostate:	n/a
31	chr12:106648541-106648591	Jurkat	blood:	n/a
32	chr12:106648541-106648591	HepG2	liver:	n/a
33	chr12:106648541-106648591	SAEC	small airway:	n/a
34	chr12:106648541-106648591	H1-hESC	embryonic stem cell:	embryo
35	chr12:106648541-106648591	PANC-1	pancreas:	n/a
36	chr12:106648541-106648591	HAEpiC	amniotic membrane:	n/a
37	chr12:106648541-106648591	ovcar-3	ovarian:	n/a
38	chr12:106648541-106648591	LNCaP	prostate:	n/a
39	chr12:106648541-106648591	Caco-2	colon:	n/a
40	chr12:106648541-106648591	Hela-S3	cervix:	n/a
41	chr12:106648541-106648591	NH-A	brain:	n/a
42	chr12:106648541-106648591	SKMC	muscle:	n/a
43	chr12:106648541-106648591	U87	brain:	n/a
44	chr12:106648541-106648591	AG10803	skin:	n/a
45	chr12:106648541-106648591	HEK293	kidney:	embryo
46	chr12:106648541-106648591	AG09309	skin:	n/a
47	chr12:106648541-106648591	AoSMC	blood vessel:	n/a
48	chr12:106648541-106648591	NB4	blood:	n/a
49	chr12:106648541-106648591	ECC-1	luminal epithelium:	n/a
50	chr12:106648541-106648591	AG04449	skin:	fetal

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106644967..106648309-chr12:106659700..106662827,5	MCF-7	breast:
3	chr12:106647187..106649805-chr12:106683824..106686258,2	MCF-7	breast:
4	chr12:106645468..106647361-chr12:106648038..106649886,2	MCF-7	breast:
5	chr12:106649519..106651023-chr12:106669984..106671532,2	MCF-7	breast:
6	chr12:106645468..106647361-chr12:106648038..106649886,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCP11L2-1	chr12:106645908-106646559	NONHSAT030477
2	lnc-TCP11L2-1	chr12:106645908-106646559	XLOC_009869

No data

Variant related genes	Relation type
CKAP4	TF binding region
CKAP4	CpG island
ENSG00000238609	chromatin interactions

Extended variants
information (count: 137 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:137 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs146524104	chr12:106646374-106646375	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs550605634	chr12:106646375-106646376	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs140858697	chr12:106646392-106646393	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs34397915	chr12:106646396-106646397	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs553563212	chr12:106646408-106646409	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs566401579	chr12:106646416-106646417	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs3741881	chr12:106646422-106646423	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs541732129	chr12:106646424-106646425	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs562598379	chr12:106646437-106646438	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs557881078	chr12:106646446-106646447	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs540775369	chr12:106646448-106646449	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs577928071	chr12:106646463-106646464	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs543553849	chr12:106646477-106646478	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs75861265	chr12:106646510-106646511	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs557078891	chr12:106646527-106646528	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs187611464	chr12:106646537-106646538	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs35013680	chr12:106646586-106646587	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs138140356	chr12:106646589-106646590	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs529836687	chr12:106646591-106646592	Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs559094865	chr12:106646611-106646612	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs2912749	chr12:106646814-106646815	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs200722238	chr12:106646818-106646819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs566486129	chr12:106646833-106646834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs149177420	chr12:106646838-106646839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs564730801	chr12:106646843-106646844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs192250207	chr12:106646912-106646913	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs184028480	chr12:106646917-106646918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs146505366	chr12:106646929-106646930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs533509461	chr12:106646930-106646931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs189609274	chr12:106646975-106646976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549619137	chr12:106646979-106646980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs566240195	chr12:106647010-106647011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs535015480	chr12:106647050-106647051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs35800222	chr12:106647076-106647077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs139276497	chr12:106647078-106647079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs571844217	chr12:106647079-106647080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs370066567	chr12:106647185-106647186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs537494078	chr12:106647225-106647226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs547318655	chr12:106647227-106647228	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12227822	chr12:106647268-106647269	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs573818416	chr12:106647276-106647277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs536313824	chr12:106647284-106647285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs552760672	chr12:106647336-106647337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs530964174	chr12:106647367-106647368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs544875569	chr12:106647371-106647372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs368560028	chr12:106647381-106647382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs180676971	chr12:106647385-106647386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs539258119	chr12:106647422-106647423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs143226686	chr12:106647486-106647487	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs73384397	chr12:106647572-106647573	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106642800-106647600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:106642800-106647800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:106642800-106648400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:106643000-106646400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:106643000-106647800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:106643200-106646600	Weak transcription	NHEK	skin
7	chr12:106643200-106647200	Weak transcription	Aorta	Aorta
8	chr12:106643200-106647800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:106643200-106647800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:106643200-106647800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:106643200-106648800	Weak transcription	Right Atrium	heart
12	chr12:106643400-106648400	Weak transcription	Fetal Lung	lung
13	chr12:106643400-106648400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:106644000-106648200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:106644200-106649800	Weak transcription	Fetal Heart	heart
16	chr12:106644400-106649400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:106645600-106647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:106645800-106647600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:106645800-106647800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:106645800-106647800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:106645800-106647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:106645800-106647800	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:106645800-106648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:106645800-106648000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:106645800-106648200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:106646000-106647600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:106646200-106646400	Weak transcription	Fetal Kidney	kidney
28	chr12:106646200-106647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:106646200-106658800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr12:106646400-106646600	ZNF genes & repeats	Fetal Kidney	kidney
31	chr12:106647600-106648800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:106647600-106649000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:106647600-106649000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:106647800-106648000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:106647800-106648000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
36	chr12:106647800-106648200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:106647800-106648600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr12:106647800-106648600	Enhancers	Fetal Muscle Leg	muscle
39	chr12:106647800-106648800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:106647800-106649000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:106647800-106649000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:106647800-106649200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr12:106647800-106649600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:106647800-106649800	Enhancers	H9 Cell Line	embryonic stem cell
45	chr12:106647800-106649800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:106648000-106648200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
47	chr12:106648000-106648400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr12:106648000-106648400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:106648000-106649000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr12:106648200-106648600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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