Variant report

Variant	nsv997896
Chromosome Location	chr2:54517853-54549501
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54534452..54537396-chr2:54540353..54542646,2	MCF-7	breast:
2	chr2:54516670..54519099-chr2:54522119..54523673,2	MCF-7	breast:
3	chr2:54516670..54519099-chr2:54522119..54523673,2	MCF-7	breast:
4	chr2:54534452..54537396-chr2:54540353..54542646,2	MCF-7	breast:
5	chr2:54503721..54505972-chr2:54523725..54525740,2	K562	blood:
6	chr2:54545854..54547406-chr2:54547534..54550529,2	MCF-7	breast:
7	chr2:54531334..54533448-chr2:54553590..54555791,2	K562	blood:
8	chr2:54545854..54547406-chr2:54547534..54550529,2	MCF-7	breast:
9	chr2:54543376..54546512-chr2:54557012..54561316,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000177994	chromatin interactions

Extended variants
information (count: 1198 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1198 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs843730	chr2:54517853-54517854	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs568287227	chr2:54517878-54517879	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs11683930	chr2:54517889-54517890	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs373474151	chr2:54517902-54517903	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs563597861	chr2:54517938-54517939	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs843731	chr2:54517956-54517957	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs183335005	chr2:54517973-54517974	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs553674377	chr2:54518024-54518025	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs11684075	chr2:54518067-54518068	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs62140508	chr2:54518068-54518069	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs144136729	chr2:54518091-54518092	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs575839244	chr2:54518155-54518156	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs544249668	chr2:54518166-54518167	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs115226032	chr2:54518172-54518173	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs533131731	chr2:54518178-54518179	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs145126615	chr2:54518185-54518186	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs187638326	chr2:54518200-54518201	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs528366959	chr2:54518240-54518241	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs114209619	chr2:54518242-54518243	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs568116066	chr2:54518249-54518250	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs530734427	chr2:54518276-54518277	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs550660841	chr2:54518290-54518291	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs548400637	chr2:54518305-54518306	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs114854453	chr2:54518406-54518407	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs116800538	chr2:54518438-54518439	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs552677895	chr2:54518461-54518462	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs566501286	chr2:54518516-54518517	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs556025661	chr2:54518572-54518573	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs575717267	chr2:54518600-54518601	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs114603088	chr2:54518618-54518619	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143116150	chr2:54518653-54518654	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs530834738	chr2:54518655-54518656	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs550538413	chr2:54518683-54518684	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs78331146	chr2:54518701-54518702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs183597864	chr2:54518716-54518717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs373728978	chr2:54518762-54518763	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs536328090	chr2:54518817-54518818	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs541717852	chr2:54518856-54518857	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs562031803	chr2:54518916-54518917	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs530696214	chr2:54518957-54518958	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs550772595	chr2:54518959-54518960	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs377398944	chr2:54518989-54518990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs370146910	chr2:54519001-54519002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs17268409	chr2:54519014-54519015	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs533048226	chr2:54519036-54519037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs546719087	chr2:54519039-54519040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs149428808	chr2:54519093-54519094	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs566294461	chr2:54519185-54519186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs535438583	chr2:54519191-54519192	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs141606911	chr2:54519265-54519266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:168 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54483400-54521200	Weak transcription	Pancreas	Pancrea
3	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:54515200-54518200	Weak transcription	Right Atrium	heart
5	chr2:54515200-54522600	Weak transcription	Psoas Muscle	Psoas
6	chr2:54515200-54526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54515400-54518000	Weak transcription	HSMMtube	muscle
8	chr2:54516000-54520200	Weak transcription	Fetal Kidney	kidney
9	chr2:54517000-54518000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr2:54517000-54518000	Enhancers	Fetal Brain Male	brain
11	chr2:54517200-54518600	Enhancers	Fetal Stomach	stomach
12	chr2:54517600-54518000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr2:54517600-54518200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr2:54517600-54518200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:54517600-54518400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:54517600-54519000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:54517600-54521800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:54517600-54536800	Weak transcription	Aorta	Aorta
19	chr2:54517800-54518000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr2:54517800-54518000	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:54517800-54518200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr2:54517800-54518200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr2:54517800-54518200	Enhancers	Brain Angular Gyrus	brain
24	chr2:54517800-54518400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
25	chr2:54517800-54537200	Weak transcription	Brain Anterior Caudate	brain
26	chr2:54518000-54518400	Enhancers	Fetal Lung	lung
27	chr2:54518000-54518400	Enhancers	HSMMtube	muscle
28	chr2:54518200-54518400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr2:54518200-54518400	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr2:54518200-54518600	Enhancers	Right Atrium	heart
31	chr2:54518400-54518600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:54518400-54518600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr2:54518400-54518800	Enhancers	Brain Angular Gyrus	brain
34	chr2:54518400-54525600	Weak transcription	HSMMtube	muscle
35	chr2:54518600-54530000	Weak transcription	Right Atrium	heart
36	chr2:54520200-54520400	Enhancers	Fetal Kidney	kidney
37	chr2:54521800-54522400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:54522000-54522400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:54522000-54522400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:54522000-54522400	Enhancers	NHEK	skin
41	chr2:54522000-54522600	Enhancers	HMEC	breast
42	chr2:54522600-54523400	Enhancers	Psoas Muscle	Psoas
43	chr2:54523000-54523400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr2:54523000-54523400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:54523000-54523400	Enhancers	Lung	lung
46	chr2:54523200-54523400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:54523200-54523400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:54523200-54523400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:54523200-54523600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:54523200-54523600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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