Variant report

Variant	esv3528510
Chromosome Location	chr15:39743685-39745883
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39719354..39722131-chr15:39742373..39743921,2	K562	blood:
2	chr15:39744731..39747916-chr15:39873044..39877161,3	MCF-7	breast:
3	chr15:39745636..39749475-chr15:39752031..39754404,4	K562	blood:
4	chr15:39742666..39745111-chr15:39746881..39749174,2	K562	blood:
5	chr15:39739352..39742846-chr15:39745277..39748876,4	MCF-7	breast:
6	chr15:39743414..39749749-chr15:39871400..39878085,10	MCF-7	breast:
7	chr15:39463804..39465395-chr15:39742405..39744124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	chromatin interactions
ENSG00000259345	chromatin interactions

Extended variants
information (count: 87 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:87 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs531062546	chr15:39743745-39743746	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs550759552	chr15:39743756-39743757	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs56370686	chr15:39743769-39743770	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs532745180	chr15:39743781-39743782	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs536458780	chr15:39743795-39743796	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs144163502	chr15:39743796-39743797	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs73397317	chr15:39743798-39743799	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs534286972	chr15:39743866-39743867	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs74010125	chr15:39743921-39743922	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs577640700	chr15:39743929-39743930	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs147803260	chr15:39743964-39743965	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs184730893	chr15:39743985-39743986	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs187738136	chr15:39744030-39744031	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs542868038	chr15:39744074-39744075	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs528037599	chr15:39744094-39744095	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs559353222	chr15:39744119-39744120	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs60154248	chr15:39744129-39744130	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs115521156	chr15:39744132-39744133	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs192402824	chr15:39744183-39744184	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs148837424	chr15:39744201-39744202	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs549417039	chr15:39744222-39744223	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs550620511	chr15:39744225-39744226	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs555639901	chr15:39744267-39744268	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs9888722	chr15:39744272-39744273	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs57291042	chr15:39744308-39744309	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs547186726	chr15:39744329-39744330	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs184802390	chr15:39744330-39744331	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs117984086	chr15:39744372-39744373	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs201967488	chr15:39744392-39744393	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs200183319	chr15:39744393-39744394	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs377233204	chr15:39744423-39744424	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs374045151	chr15:39744496-39744497	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs370068212	chr15:39744505-39744506	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs1842040	chr15:39744566-39744567	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs79260862	chr15:39744591-39744592	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs557067242	chr15:39744622-39744623	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs573798423	chr15:39744685-39744686	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs542829333	chr15:39744793-39744794	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs376945182	chr15:39744850-39744851	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs11070203	chr15:39744859-39744860	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs181812903	chr15:39744905-39744906	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs150983705	chr15:39744965-39744966	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs545328463	chr15:39744973-39744974	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs140900079	chr15:39745010-39745011	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs575194298	chr15:39745039-39745040	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs373166054	chr15:39745083-39745084	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs544220948	chr15:39745087-39745088	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs144868579	chr15:39745096-39745097	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs530167013	chr15:39745097-39745098	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs546855234	chr15:39745100-39745101	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
HDAC8	0	CNVD
NIPBL	0	CNVD
RAD21	0	CNVD
SMC1A	0	CNVD
SMC3	0	CNVD
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Angelman syndrome	16183798	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16774939	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21785460	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Autism	19204725	CNVD
Schizophrenia	19204725	CNVD
Schizophrenia	19149910	CNVD
Ovarian cancer	22174824	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	17440070	CNVD
Basal cell lymphoma	17053054	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Cancer	20164920	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21129771	CNVD
Breast cancer	21045282	CNVD
Papillary thyroid carcinoma	22161024	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Ovarian cancer	21720365	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39727200-39746800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:39740400-39745400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:39740400-39745400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:39740400-39747200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:39740800-39745400	Weak transcription	GM12878-XiMat	blood
7	chr15:39742400-39744200	Enhancers	Fetal Stomach	stomach
8	chr15:39742400-39744400	Enhancers	Fetal Lung	lung
9	chr15:39742400-39744600	Enhancers	Rectal Smooth Muscle	rectum
10	chr15:39742600-39744200	Enhancers	Colon Smooth Muscle	Colon
11	chr15:39742800-39744200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr15:39743000-39745400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:39743000-39745600	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:39743200-39744000	Enhancers	NHLF	lung
15	chr15:39743200-39744200	Enhancers	Small Intestine	intestine
16	chr15:39743200-39744200	Enhancers	NHDF-Ad	bronchial
17	chr15:39743400-39744200	Enhancers	Duodenum Mucosa	Duodenum
18	chr15:39743400-39744400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr15:39743600-39743800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:39743600-39743800	Enhancers	Osteobl	bone
21	chr15:39743800-39744200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:39743800-39744600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:39743800-39745400	Weak transcription	Osteobl	bone
24	chr15:39743800-39745600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:39744000-39745000	Enhancers	HUVEC	blood vessel
26	chr15:39744000-39747600	Weak transcription	NHLF	lung
27	chr15:39744200-39745200	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:39744200-39745200	Weak transcription	Fetal Stomach	stomach
29	chr15:39744200-39745600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:39744200-39745600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:39744200-39745600	Weak transcription	NHDF-Ad	bronchial
32	chr15:39744400-39745400	Weak transcription	Fetal Lung	lung
33	chr15:39744400-39748400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:39744600-39745800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:39744600-39753400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:39745200-39745600	Enhancers	Colon Smooth Muscle	Colon
37	chr15:39745200-39746600	Enhancers	Fetal Stomach	stomach
38	chr15:39745200-39747400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:39745400-39745600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr15:39745400-39745600	Enhancers	GM12878-XiMat	blood
41	chr15:39745400-39745800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr15:39745400-39746200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr15:39745400-39746800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr15:39745400-39746800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:39745400-39747400	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr15:39745400-39747800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr15:39745400-39748800	Enhancers	Osteobl	bone
48	chr15:39745400-39749600	Enhancers	Fetal Lung	lung
49	chr15:39745600-39745800	Enhancers	NH-A	brain
50	chr15:39745600-39746000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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