Variant report

Variant	nsv557372
Chromosome Location	chr12:9555588-9558905
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PZP-12	chr12:9558904-9559128	NONHSAT026823

Extended variants
information (count: 208 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:208 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs199985355	chr12:9555591-9555592	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs543374956	chr12:9555597-9555598	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs192980192	chr12:9555604-9555605	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs114665079	chr12:9555609-9555610	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs368324425	chr12:9555621-9555622	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs113016109	chr12:9555623-9555624	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs200868444	chr12:9555624-9555625	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs191447215	chr12:9555642-9555643	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs60520691	chr12:9555665-9555666	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs184912263	chr12:9555672-9555673	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs112896161	chr12:9555680-9555681	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs78363881	chr12:9555705-9555706	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs77164630	chr12:9555706-9555707	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs76788670	chr12:9555710-9555711	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs559681317	chr12:9555716-9555717	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs184759880	chr12:9555727-9555728	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs547500283	chr12:9555736-9555737	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs74192474	chr12:9555758-9555759	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs111466002	chr12:9555766-9555767	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs202038993	chr12:9555794-9555795	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs189529888	chr12:9555801-9555802	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
22	rs199765431	chr12:9555812-9555813	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
23	rs181513985	chr12:9555816-9555817	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
24	rs187098742	chr12:9555827-9555828	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
25	rs189518826	chr12:9555843-9555844	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
26	rs148228982	chr12:9555864-9555865	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
27	rs71441752	chr12:9555877-9555878	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
28	rs71441751	chr12:9555879-9555880	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
29	rs549208888	chr12:9555888-9555889	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
30	rs71441750	chr12:9555896-9555897	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
31	rs71441749	chr12:9555901-9555902	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
32	rs61914450	chr12:9555934-9555935	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs61914451	chr12:9555937-9555938	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs115248798	chr12:9555944-9555945	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
35	rs537048655	chr12:9555974-9555975	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
36	rs113910830	chr12:9555980-9555981	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
37	rs114481207	chr12:9555987-9555988	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
38	rs185949636	chr12:9556008-9556009	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
39	rs141198189	chr12:9556011-9556012	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
40	rs113512093	chr12:9556017-9556018	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
41	rs573494541	chr12:9556030-9556031	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
42	rs189550872	chr12:9556031-9556032	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
43	rs545590906	chr12:9556041-9556042	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
44	rs182245475	chr12:9556047-9556048	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
45	rs186134372	chr12:9556056-9556057	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
46	rs564174910	chr12:9556086-9556087	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
47	rs190997775	chr12:9556098-9556099	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
48	rs183362060	chr12:9556117-9556118	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
49	rs111839455	chr12:9556120-9556121	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
50	rs549791575	chr12:9556145-9556146	Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Epilepsy	21858020	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
craniofacial dysmorphism	21918468	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Alzheimer''s disease	17160897	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	21611746	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
early-passage human iPS cells	21368824	CNVD
Obesity	21131291	CNVD
small cell lung cancer	20016488	CNVD
Incontinentia Pigmenti	22033527	CNVD
Oligozoospermia	20877625	CNVD
Sertoli-cell only syndrome	20877625	CNVD
Cancer	21272361	CNVD
Schizophrenia	20967226	CNVD

Chromatin state (count:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9541400-9557200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:9541800-9557400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:9542800-9555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:9544800-9593200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:9545400-9573800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:9545400-9575600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:9545600-9555600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:9545800-9555600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:9546000-9555600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:9546200-9559400	Weak transcription	A549	lung
11	chr12:9547000-9558600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:9547200-9556800	Weak transcription	Fetal Stomach	stomach
13	chr12:9547400-9556600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:9547400-9557400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:9549400-9555600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:9549400-9558800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9549400-9559200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:9549400-9564000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:9551400-9557000	Weak transcription	Dnd41	blood
20	chr12:9554600-9555800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:9555200-9556200	Active TSS	Right Ventricle	heart
22	chr12:9555200-9557600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:9555400-9555600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:9555400-9555600	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:9555400-9555600	Enhancers	Colonic Mucosa	Colon
26	chr12:9555400-9555600	Flanking Active TSS	Thymus	Thymus
27	chr12:9555400-9555800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr12:9555400-9555800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:9555400-9555800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:9555400-9555800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:9555400-9555800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:9555400-9555800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr12:9555400-9555800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
34	chr12:9555400-9555800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
35	chr12:9555400-9555800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:9555400-9556000	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:9555400-9556000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr12:9555600-9555800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:9555600-9555800	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr12:9555600-9555800	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:9555600-9555800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:9555600-9555800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr12:9555600-9556000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
44	chr12:9555600-9556000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:9555600-9556000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:9555600-9556200	Active TSS	Thymus	Thymus
47	chr12:9555600-9559400	Weak transcription	Colonic Mucosa	Colon
48	chr12:9555800-9556000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr12:9555800-9556200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:9555800-9557400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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