Variant report

Variant	esv3404975
Chromosome Location	chr12:619291-624289
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:618073..620518-chr12:625351..628084,2	MCF-7	breast:
2	chr12:623934..625776-chr12:628238..630617,2	MCF-7	breast:
3	chr12:622362..623146-chr12:632963..633907,2	MCF-7	breast:
4	chr12:610332..613763-chr12:616552..619652,4	MCF-7	breast:
5	chr12:622277..623146-chr12:632963..633980,6	MCF-7	breast:
6	chr12:622355..623083-chr12:633209..633927,4	MCF-7	breast:
7	chr12:618074..619807-chr12:641547..643283,2	MCF-7	breast:
8	chr12:617937..620233-chr12:642508..644938,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC77-2	chr12:623386-625305	ucscGeneNc_uc009zdl_1
2	lnc-CCDC77-2	chr12:622408-623144	ucscGeneNc_uc009zdl_1

No data

Extended variants
information (count: 307 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:307 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549593256	chr12:619302-619303	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs567516582	chr12:619317-619318	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs531744849	chr12:619380-619381	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs139332166	chr12:619447-619448	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs188027135	chr12:619452-619453	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs75735245	chr12:619461-619462	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs550953554	chr12:619490-619491	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs11063334	chr12:619526-619527	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs76158258	chr12:619550-619551	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
10	rs373576541	chr12:619554-619555	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs57794713	chr12:619559-619560	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs547497720	chr12:619570-619571	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs144969025	chr12:619574-619575	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs576311132	chr12:619594-619595	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181908572	chr12:619601-619602	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs556714060	chr12:619607-619608	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs549996742	chr12:619610-619611	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs367667505	chr12:619613-619614	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs386759353	chr12:619616-619617	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs545417555	chr12:619617-619618	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs11830324	chr12:619618-619619	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs376833030	chr12:619647-619648	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs137915117	chr12:619661-619662	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs556557465	chr12:619668-619669	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs149058358	chr12:619690-619691	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs554448399	chr12:619711-619712	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs566200504	chr12:619712-619713	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs376779436	chr12:619717-619718	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs113212128	chr12:619727-619728	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs368418855	chr12:619755-619756	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs111980826	chr12:619758-619759	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs368360187	chr12:619769-619770	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs542955192	chr12:619792-619793	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs7306988	chr12:619808-619809	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs186081456	chr12:619814-619815	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs549935509	chr12:619824-619825	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs75503888	chr12:619862-619863	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532094993	chr12:619900-619901	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs543988236	chr12:619906-619907	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547412265	chr12:619917-619918	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs77637096	chr12:619968-619969	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs11608540	chr12:619995-619996	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs536592506	chr12:620031-620032	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs80064494	chr12:620091-620092	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs190690656	chr12:620134-620135	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs537117981	chr12:620142-620143	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs576648070	chr12:620144-620145	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs115805081	chr12:620160-620161	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs368716576	chr12:620179-620180	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs113711006	chr12:620182-620183	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
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
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Autism	22495309	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Melanoma	20877625	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:616000-620600	Enhancers	Fetal Heart	heart
2	chr12:616400-619600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:616400-619800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:616400-620200	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr12:616400-620400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:616600-620600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:616600-620600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:617200-620600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:617600-620000	Enhancers	Left Ventricle	heart
10	chr12:617800-619600	Enhancers	Gastric	stomach
11	chr12:617800-619800	Enhancers	Right Ventricle	heart
12	chr12:617800-620000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr12:617800-620000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr12:617800-620200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:617800-620200	Enhancers	Duodenum Mucosa	Duodenum
16	chr12:617800-620400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:617800-620400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:617800-620600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:618000-619400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:618000-619800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:618000-619800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:618000-619800	Enhancers	Fetal Muscle Leg	muscle
23	chr12:618000-619800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr12:618000-620200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr12:618000-620200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:618000-620600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr12:618000-620800	Enhancers	Fetal Kidney	kidney
28	chr12:618200-619600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:618200-619600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:618200-619600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:618200-619600	Enhancers	Esophagus	oesophagus
32	chr12:618200-619600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:618200-620000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:618200-620000	Enhancers	Fetal Intestine Small	intestine
35	chr12:618200-620800	Enhancers	Pancreas	Pancrea
36	chr12:618400-619600	Enhancers	Fetal Thymus	thymus
37	chr12:618400-619600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:618400-619800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr12:618400-620000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:618600-619400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:618600-619600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:618600-619600	Enhancers	Right Atrium	heart
43	chr12:618600-619600	Flanking Active TSS	NHEK	skin
44	chr12:618600-619800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:618800-619400	Genic enhancers	Stomach Mucosa	stomach
46	chr12:618800-619600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:618800-619600	Enhancers	NH-A	brain
48	chr12:618800-620000	Enhancers	Brain Cingulate Gyrus	brain
49	chr12:618800-620200	Enhancers	Brain Substantia Nigra	brain
50	chr12:618800-620200	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links