Variant report

Variant	esv3339510
Chromosome Location	chr12:48448935-48452108
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr12:48449277-48449285	A549	lung:	n/a	n/a
2	BRCA1	chr12:48449053-48449071	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:48448732-48448937	ProgFib	skin:	n/a	n/a
4	POLR2A	chr12:48449208-48449209	MCF-7	breast:	n/a	n/a
5	POLR2A	chr12:48448938-48448954	ProgFib	skin:	n/a	n/a
6	STAT3	chr12:48449204-48449401	MCF10A-Er-Src	breast:	n/a	n/a
7	ZNF274	chr12:48448996-48450212	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48446661..48450217-chr12:48458596..48461556,3	K562	blood:
2	chr12:48435313..48437988-chr12:48451982..48454529,2	K562	blood:
3	chr12:48448475..48449474-chr5:40834158..40834864,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1-228P16.5.1-2	chr12:48448754-48449036	NONHSAT140070
2	lnc-RP1-228P16.5.1-2	chr12:48448596-48449374	NONHSAT027976

No data

Variant related genes	Relation type
ENSG00000240399	TF binding region
ENSG00000079387	chromatin interactions
ENSG00000145592	chromatin interactions

Extended variants
information (count: 151 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:151 , 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	rs560564534	chr12:48448986-48448987	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs76795225	chr12:48449022-48449023	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs201927081	chr12:48449026-48449027	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs77590573	chr12:48449047-48449048	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	mRNA abundance
5	rs537726375	chr12:48449053-48449054	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs568816520	chr12:48449054-48449055	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs562792022	chr12:48449061-48449062	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs530626214	chr12:48449076-48449077	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs550401273	chr12:48449113-48449114	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs4760677	chr12:48449163-48449164	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs571122039	chr12:48449221-48449222	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
12	rs75064228	chr12:48449224-48449225	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	mRNA abundance
13	rs78773707	chr12:48449233-48449234	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
14	rs566479457	chr12:48449235-48449236	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
15	rs538229565	chr12:48449247-48449248	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
16	rs558623249	chr12:48449262-48449263	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
17	rs111822247	chr12:48449273-48449274	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
18	rs537933329	chr12:48449305-48449306	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
19	rs117206241	chr12:48449309-48449310	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
20	rs189733225	chr12:48449327-48449328	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
21	rs149294089	chr12:48449386-48449387	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs560593214	chr12:48449411-48449412	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs368684834	chr12:48449435-48449436	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs7978968	chr12:48449446-48449447	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs545835421	chr12:48449482-48449483	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs542780106	chr12:48449504-48449505	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs144742303	chr12:48449624-48449625	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs531738682	chr12:48449768-48449769	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs548255239	chr12:48449795-48449796	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs368701270	chr12:48449922-48449923	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs373473559	chr12:48449928-48449929	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs181649284	chr12:48449938-48449939	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs58575922	chr12:48449957-48449958	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs56967342	chr12:48449959-48449960	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs59900920	chr12:48449966-48449967	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs55669205	chr12:48449973-48449974	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs55707747	chr12:48449976-48449977	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs61401624	chr12:48449991-48449992	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs55671810	chr12:48449992-48449993	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs61495049	chr12:48449998-48449999	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs61721944	chr12:48450026-48450027	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs28972821	chr12:48450029-48450030	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs61728369	chr12:48450038-48450039	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs56044081	chr12:48450039-48450040	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs574094183	chr12:48450045-48450046	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs28970801	chr12:48450048-48450049	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs28972741	chr12:48450054-48450055	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs189468509	chr12:48450056-48450057	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs28972363	chr12:48450060-48450061	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs28971727	chr12:48450065-48450066	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
Breast cancer	22522925	CNVD

Chromatin state (count:182 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
5	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48435800-48452400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:48439200-48453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48439200-48456800	Weak transcription	HMEC	breast
10	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
12	chr12:48440000-48452200	Weak transcription	NHDF-Ad	bronchial
13	chr12:48440000-48454000	Weak transcription	HUVEC	blood vessel
14	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:48440200-48452600	Weak transcription	Brain Germinal Matrix	brain
16	chr12:48440200-48452600	Weak transcription	Right Ventricle	heart
17	chr12:48440200-48453800	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:48440400-48453400	Weak transcription	Esophagus	oesophagus
19	chr12:48440800-48452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:48440800-48452400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:48441000-48452600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:48441200-48452400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48441200-48457000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:48441400-48452400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:48441400-48453400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48441400-48453400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:48441400-48454400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
29	chr12:48441600-48452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48441600-48452400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:48441600-48452400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:48441600-48452800	Weak transcription	NHEK	skin
33	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:48442000-48452200	Weak transcription	Fetal Brain Female	brain
35	chr12:48442000-48452400	Weak transcription	Fetal Kidney	kidney
36	chr12:48442200-48452400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:48442400-48452600	Weak transcription	Fetal Brain Male	brain
38	chr12:48442800-48452400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:48443000-48452200	Weak transcription	HepG2	liver
40	chr12:48443000-48452200	Weak transcription	NH-A	brain
41	chr12:48443000-48453200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:48443200-48452400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:48443400-48449000	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:48443400-48452000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:48443400-48452200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:48443400-48452400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:48443400-48452400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:48443400-48453400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:48443400-48453600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links