Variant report

Variant	esv1794366
Chromosome Location	chr5:52240421-52249476
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:14)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52244525..52246067-chr5:52384828..52387820,2	MCF-7	breast:
2	chr5:52244273..52246874-chr5:52284639..52287119,3	MCF-7	breast:
3	chr5:52239227..52240957-chr5:52240958..52243466,2	MCF-7	breast:
4	chr5:52244476..52245215-chr5:52391489..52392462,3	MCF-7	breast:
5	chr5:52244011..52244957-chr5:52391475..52392472,7	K562	blood:
6	chr5:52242586..52243458-chr5:52411210..52411778,2	MCF-7	breast:
7	chr5:52246465..52248425-chr5:52385773..52388530,2	MCF-7	breast:
8	chr5:52240942..52242706-chr5:52367816..52370164,2	MCF-7	breast:
9	chr5:52243837..52246026-chr5:52316094..52318313,2	MCF-7	breast:
10	chr5:52082533..52083427-chr5:52240291..52241141,2	MCF-7	breast:
11	chr5:52243208..52246085-chr5:52282017..52284486,2	MCF-7	breast:
12	chr5:52244780..52247572-chr5:52249796..52252128,2	K562	blood:
13	chr5:52239227..52240957-chr5:52240958..52243466,2	MCF-7	breast:
14	chr5:52244044..52244891-chr5:52391492..52392380,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOCS2-1	chr5:52244655-52244737	ENSG00000249899.1
2	lnc-MOCS2-1	chr5:52244655-52244737	ENSG00000249899.1

No data

Variant related genes	Relation type
ENSG00000272123	chromatin interactions
ENSG00000249899	chromatin interactions
ENSG00000164171	chromatin interactions

Extended variants
information (count: 343 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:343 , 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	rs10071067	chr5:52240421-52240422	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs548205979	chr5:52240444-52240445	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs16880544	chr5:52240466-52240467	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs1363189	chr5:52240476-52240477	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs1363188	chr5:52240491-52240492	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs576818835	chr5:52240495-52240496	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs534850971	chr5:52240525-52240526	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs142971593	chr5:52240552-52240553	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs574967802	chr5:52240636-52240637	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs542375678	chr5:52240653-52240654	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs75347143	chr5:52240694-52240695	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs575959520	chr5:52240720-52240721	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs543449105	chr5:52240741-52240742	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs79744792	chr5:52240744-52240745	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs532124874	chr5:52240752-52240753	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs547213289	chr5:52240758-52240759	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs181135464	chr5:52240772-52240773	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs143105379	chr5:52240775-52240776	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs369397740	chr5:52240783-52240784	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs548318871	chr5:52240798-52240799	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs988574	chr5:52240810-52240811	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs185220542	chr5:52240829-52240830	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs151102756	chr5:52240850-52240851	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs370267435	chr5:52240872-52240873	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs189693344	chr5:52240887-52240888	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs372340889	chr5:52240896-52240897	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs111916291	chr5:52240904-52240905	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs369048591	chr5:52240906-52240907	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs553207336	chr5:52240926-52240927	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs574844464	chr5:52240934-52240935	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs142523147	chr5:52240974-52240975	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs182357508	chr5:52240991-52240992	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs369172424	chr5:52241103-52241104	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs556441445	chr5:52241120-52241121	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs187423403	chr5:52241137-52241138	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs141047272	chr5:52241227-52241228	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs374724437	chr5:52241257-52241258	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs546550038	chr5:52241286-52241287	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs1421928	chr5:52241332-52241333	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs371336306	chr5:52241354-52241355	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs553208258	chr5:52241384-52241385	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs6859171	chr5:52241438-52241439	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs540996637	chr5:52241441-52241442	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs150235402	chr5:52241452-52241453	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs191839869	chr5:52241563-52241564	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs16880552	chr5:52241584-52241585	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs563191046	chr5:52241612-52241613	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs530596601	chr5:52241644-52241645	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs561577757	chr5:52241724-52241725	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs530285232	chr5:52241753-52241754	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Cancer	16751803	CNVD
Autism	22495311	CNVD
Intellectual disability	22102821	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	20729466	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	21911935	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:296 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52206400-52240800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:52211600-52244400	Weak transcription	HepG2	liver
4	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
5	chr5:52218800-52240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:52219200-52240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52219200-52240800	Weak transcription	NHLF	lung
8	chr5:52220000-52243000	Weak transcription	Gastric	stomach
9	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:52221400-52240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
13	chr5:52227000-52240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:52228400-52240800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
17	chr5:52232200-52240600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
19	chr5:52235000-52240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:52235400-52243200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:52236000-52240800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:52237000-52240800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:52237400-52240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:52237400-52240800	Weak transcription	Adipose Nuclei	Adipose
25	chr5:52238800-52252200	Strong transcription	Liver	Liver
26	chr5:52239600-52240800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:52239800-52240800	Weak transcription	Right Atrium	heart
28	chr5:52240000-52240800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:52240000-52240800	Enhancers	Dnd41	blood
30	chr5:52240000-52245400	Weak transcription	Placenta	Placenta
31	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
32	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
33	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
34	chr5:52240000-52253600	Weak transcription	Lung	lung
35	chr5:52240200-52241200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr5:52240200-52244200	Weak transcription	Fetal Lung	lung
37	chr5:52240200-52244200	Weak transcription	Fetal Stomach	stomach
38	chr5:52240200-52247000	Weak transcription	Fetal Muscle Leg	muscle
39	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
40	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
41	chr5:52240400-52240600	Enhancers	NHDF-Ad	bronchial
42	chr5:52240400-52240800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:52240400-52240800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:52240400-52240800	Enhancers	Osteobl	bone
45	chr5:52240400-52241200	Active TSS	Stomach Smooth Muscle	stomach
46	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
47	chr5:52240600-52240800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:52240600-52240800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr5:52240600-52240800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:52240600-52240800	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links