Variant report

Variant	nsv591394
Chromosome Location	chr3:120163440-120164873
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120162045..120164742-chr3:120177102..120179636,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:43 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547144095	chr3:120163535-120163536	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs1259331	chr3:120163606-120163607	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs148622585	chr3:120163643-120163644	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs552201152	chr3:120163654-120163655	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs201145851	chr3:120163669-120163670	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs142053213	chr3:120163724-120163725	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs554821485	chr3:120163726-120163727	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs574520988	chr3:120163727-120163728	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs534099828	chr3:120163757-120163758	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs553819995	chr3:120163896-120163897	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs1259332	chr3:120163932-120163933	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs545819939	chr3:120163941-120163942	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs147964791	chr3:120164021-120164022	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs116398462	chr3:120164067-120164068	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs541892165	chr3:120164111-120164112	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs112943892	chr3:120164119-120164120	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs535851637	chr3:120164148-120164149	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs561140086	chr3:120164150-120164151	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs548571526	chr3:120164242-120164243	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs1259333	chr3:120164287-120164288	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs547962911	chr3:120164304-120164305	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6768839	chr3:120164314-120164315	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs76295980	chr3:120164319-120164320	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs36029707	chr3:120164348-120164349	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs375341279	chr3:120164362-120164363	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs565130532	chr3:120164411-120164412	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs552238292	chr3:120164421-120164422	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs141879742	chr3:120164528-120164529	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs147104748	chr3:120164537-120164538	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs184640417	chr3:120164554-120164555	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs568135089	chr3:120164623-120164624	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs79154925	chr3:120164641-120164642	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs374907066	chr3:120164696-120164697	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs533791251	chr3:120164699-120164700	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs114711679	chr3:120164725-120164726	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs189189505	chr3:120164751-120164752	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs115269531	chr3:120164774-120164775	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs180928401	chr3:120164796-120164797	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs574693550	chr3:120164799-120164800	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs575982135	chr3:120164800-120164801	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs541928936	chr3:120164825-120164826	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs184125743	chr3:120164834-120164835	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs572499870	chr3:120164873-120164874	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:131 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:120138200-120169200	Weak transcription	Gastric	stomach
3	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
5	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:120155800-120168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120156200-120166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:120156600-120168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:120156800-120165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:120156800-120166000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:120158000-120166200	Weak transcription	Fetal Brain Female	brain
13	chr3:120158000-120167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:120158200-120167400	Weak transcription	Brain Germinal Matrix	brain
15	chr3:120158400-120165600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:120158800-120165200	Weak transcription	Lung	lung
17	chr3:120158800-120166000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:120158800-120167400	Weak transcription	A549	lung
19	chr3:120159600-120165200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:120159600-120165800	Weak transcription	Spleen	Spleen
21	chr3:120159800-120164600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:120159800-120165000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:120160000-120164600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:120160000-120167400	Weak transcription	HMEC	breast
25	chr3:120160000-120167600	Weak transcription	NHEK	skin
26	chr3:120160200-120164600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:120160200-120165000	Enhancers	Colon Smooth Muscle	Colon
28	chr3:120160400-120164400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:120160400-120165800	Weak transcription	Placenta	Placenta
30	chr3:120160600-120164600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:120160600-120165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:120160600-120165200	Enhancers	Fetal Heart	heart
33	chr3:120160600-120165800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:120160600-120166000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:120160600-120167400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:120160800-120166000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:120160800-120166000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:120160800-120166200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:120160800-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:120160800-120167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:120161000-120165400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:120161000-120166000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:120161000-120167400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:120161200-120165200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:120161200-120165200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:120161200-120166000	Weak transcription	Brain Angular Gyrus	brain
47	chr3:120161200-120167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:120161400-120164600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:120161400-120164600	Weak transcription	Brain Anterior Caudate	brain
50	chr3:120161400-120164600	Weak transcription	Fetal Muscle Leg	muscle

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