Variant report

Variant	esv2760677
Chromosome Location	chr12:48412410-48416967
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:20)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
2	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:
3	chr12:48411445..48413421-chr12:48418888..48421614,3	MCF-7	breast:
4	chr12:48407869..48410123-chr12:48411477..48413880,2	K562	blood:
5	chr12:48292355..48294336-chr12:48414292..48417246,2	MCF-7	breast:
6	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
7	chr12:48416195..48418689-chr12:48432533..48434686,2	K562	blood:
8	chr12:48367607..48371765-chr12:48415495..48417356,3	MCF-7	breast:
9	chr12:48416842..48418454-chr12:48435864..48437741,2	MCF-7	breast:
10	chr12:48212416..48215175-chr12:48415223..48418079,4	MCF-7	breast:
11	chr12:48407751..48410923-chr12:48414618..48417182,4	MCF-7	breast:
12	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
13	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:
14	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
15	chr12:48395740..48398491-chr12:48410326..48412487,2	MCF-7	breast:
16	chr12:48357498..48359897-chr12:48415530..48417456,2	MCF-7	breast:
17	chr12:48415871..48417650-chr12:48439843..48442703,2	MCF-7	breast:
18	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:
19	chr12:48416900..48419304-chr12:48549157..48552214,3	MCF-7	breast:
20	chr12:48294511..48296971-chr12:48414193..48417151,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-1	chr12:48416618-48419252	ENSG00000257985.1

No data

Variant related genes	Relation type
ENSG00000257955	chromatin interactions
ENSG00000134291	chromatin interactions
ENSG00000061273	chromatin interactions
ENSG00000139219	chromatin interactions
ENSG00000177981	chromatin interactions

Extended variants
information (count: 185 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:185 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17122565	chr12:48412410-48412411	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs552694041	chr12:48412439-48412440	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs200089050	chr12:48412444-48412445	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs202224091	chr12:48412445-48412446	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs200683038	chr12:48412446-48412447	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs398116416	chr12:48412447-48412448	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs398055551	chr12:48412459-48412460	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs375353923	chr12:48412460-48412461	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs143619866	chr12:48412487-48412488	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs148050736	chr12:48412522-48412523	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs559081906	chr12:48412536-48412537	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs78239819	chr12:48412550-48412551	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
13	rs544852204	chr12:48412569-48412570	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs2079295	chr12:48412592-48412593	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs74086502	chr12:48412600-48412601	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs540610676	chr12:48412605-48412606	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs374717888	chr12:48412607-48412608	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs560604611	chr12:48412646-48412647	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs532618279	chr12:48412648-48412649	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs60898235	chr12:48412695-48412696	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs74090303	chr12:48412733-48412734	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs565044358	chr12:48412765-48412766	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs541425475	chr12:48412791-48412792	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs568630730	chr12:48412800-48412801	Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs530723213	chr12:48412803-48412804	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs550890978	chr12:48412843-48412844	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs559542247	chr12:48412879-48412880	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs74090304	chr12:48412897-48412898	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs12581263	chr12:48412942-48412943	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs546170642	chr12:48412963-48412964	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs78327232	chr12:48412984-48412985	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs530214676	chr12:48413005-48413006	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs184693731	chr12:48413011-48413012	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs10160938	chr12:48413046-48413047	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs571934563	chr12:48413106-48413107	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs569477904	chr12:48413139-48413140	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs188308452	chr12:48413163-48413164	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs555272773	chr12:48413223-48413224	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs575172278	chr12:48413230-48413231	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs534201397	chr12:48413245-48413246	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs180777551	chr12:48413262-48413263	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs570734240	chr12:48413274-48413275	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs76841481	chr12:48413369-48413370	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
44	rs185576024	chr12:48413378-48413379	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs562830886	chr12:48413414-48413415	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs575440460	chr12:48413423-48413424	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs544051127	chr12:48413427-48413428	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs189723188	chr12:48413460-48413461	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs529901454	chr12:48413467-48413468	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs546193203	chr12:48413497-48413498	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	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
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	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
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Anaplastic thyroid cancer	18753363	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
3	chr12:48411400-48412600	Enhancers	HepG2	liver
4	chr12:48411600-48415000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48411600-48415200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48412000-48415800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:48412200-48412800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:48412400-48412600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:48412400-48415000	Weak transcription	Fetal Intestine Large	intestine
10	chr12:48412400-48415000	Weak transcription	Fetal Intestine Small	intestine
11	chr12:48412400-48415000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:48412600-48415400	Weak transcription	HepG2	liver
13	chr12:48413400-48413600	Enhancers	Right Ventricle	heart
14	chr12:48413600-48415400	Weak transcription	Right Ventricle	heart
15	chr12:48414800-48415000	Enhancers	Hela-S3	cervix
16	chr12:48414800-48415600	Enhancers	Left Ventricle	heart
17	chr12:48415000-48415200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:48415000-48415200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:48415000-48415400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:48415000-48416000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:48415000-48416000	Flanking Active TSS	Hela-S3	cervix
22	chr12:48415000-48416800	Enhancers	Right Atrium	heart
23	chr12:48415000-48417800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:48415000-48417800	Enhancers	Fetal Lung	lung
25	chr12:48415000-48417800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr12:48415000-48418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:48415000-48418200	Enhancers	Fetal Intestine Large	intestine
28	chr12:48415000-48418200	Enhancers	Fetal Intestine Small	intestine
29	chr12:48415200-48415400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr12:48415200-48415600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:48415200-48416000	Enhancers	Gastric	stomach
32	chr12:48415200-48416800	Enhancers	Placenta	Placenta
33	chr12:48415200-48418000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:48415200-48418200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:48415400-48415600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:48415400-48415600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr12:48415400-48415600	Enhancers	Pancreas	Pancrea
38	chr12:48415400-48415600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:48415400-48415800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:48415400-48417000	Enhancers	Right Ventricle	heart
41	chr12:48415400-48417800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:48415400-48417800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
43	chr12:48415400-48418000	Enhancers	Fetal Heart	heart
44	chr12:48415400-48418000	Enhancers	HepG2	liver
45	chr12:48415600-48415800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:48415600-48415800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:48415600-48415800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr12:48415600-48415800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:48415600-48415800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:48415600-48415800	Bivalent Enhancer	Fetal Stomach	stomach

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