Variant report

Variant	esv3495340
Chromosome Location	chr12:9559050-9561306
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
2	lnc-PZP-12	chr12:9559865-9560050	NONHSAT026823

Extended variants
information (count: 104 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:104 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12372638	chr12:9559056-9559057	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	mRNA abundance
2	rs12370610	chr12:9559064-9559065	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
3	rs35701654	chr12:9559078-9559079	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
4	rs12824085	chr12:9559079-9559080	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	mRNA abundance
5	rs146610213	chr12:9559115-9559116	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
6	rs193050450	chr12:9559125-9559126	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
7	rs150296058	chr12:9559133-9559134	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
8	rs575497655	chr12:9559138-9559139	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
9	rs201675890	chr12:9559141-9559142	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
10	rs138065946	chr12:9559168-9559169	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
11	rs59315733	chr12:9559176-9559177	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
12	rs544476340	chr12:9559188-9559189	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
13	rs375223779	chr12:9559190-9559191	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
14	rs560962223	chr12:9559195-9559196	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
15	rs369481778	chr12:9559251-9559252	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs61914452	chr12:9559289-9559290	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs373482116	chr12:9559323-9559324	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs375336631	chr12:9559345-9559346	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs540403853	chr12:9559353-9559354	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs184425099	chr12:9559356-9559357	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs188482126	chr12:9559359-9559360	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs181325383	chr12:9559373-9559374	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs66661587	chr12:9559407-9559408	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
24	rs112222899	chr12:9559424-9559425	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
25	rs546258094	chr12:9559426-9559427	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
26	rs113288828	chr12:9559480-9559481	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
27	rs562895657	chr12:9559486-9559487	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
28	rs367753984	chr12:9559509-9559510	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
29	rs372475318	chr12:9559542-9559543	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
30	rs531939088	chr12:9559559-9559560	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
31	rs113494068	chr12:9559575-9559576	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
32	rs183608691	chr12:9559584-9559585	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
33	rs189266989	chr12:9559608-9559609	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
34	rs180898517	chr12:9559635-9559636	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
35	rs187248724	chr12:9559642-9559643	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
36	rs568295322	chr12:9559647-9559648	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
37	rs376954700	chr12:9559654-9559655	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
38	rs370635320	chr12:9559659-9559660	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
39	rs114752948	chr12:9559678-9559679	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
40	rs548846780	chr12:9559702-9559703	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
41	rs568625478	chr12:9559720-9559721	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
42	rs527900879	chr12:9559727-9559728	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
43	rs377676513	chr12:9559732-9559733	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
44	rs566272033	chr12:9559743-9559744	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
45	rs192035894	chr12:9559761-9559762	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
46	rs181749933	chr12:9559762-9559763	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
47	rs370878472	chr12:9559829-9559830	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs150825435	chr12:9559890-9559891	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs200944525	chr12:9559897-9559898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs139234127	chr12:9559928-9559929	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription	lncRNA	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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9544800-9593200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:9545400-9573800	Weak transcription	Fetal Intestine Small	intestine
3	chr12:9545400-9575600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:9546200-9559400	Weak transcription	A549	lung
5	chr12:9549400-9559200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:9549400-9564000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:9555600-9559400	Weak transcription	Colonic Mucosa	Colon
8	chr12:9557400-9559200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:9557400-9559400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:9557400-9564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:9557600-9559800	Enhancers	Fetal Brain Male	brain
12	chr12:9557600-9564200	Weak transcription	Dnd41	blood
13	chr12:9557600-9572200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:9557800-9559400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:9557800-9571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:9558200-9560000	Active TSS	Right Ventricle	heart
17	chr12:9558400-9559600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:9558400-9559600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:9558400-9559600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:9558400-9559600	ZNF genes & repeats	Fetal Thymus	thymus
21	chr12:9558600-9559600	Active TSS	Brain Hippocampus Middle	brain
22	chr12:9558600-9559600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr12:9558600-9559600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
24	chr12:9558600-9559800	Active TSS	Fetal Brain Female	brain
25	chr12:9558600-9559800	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:9558600-9560000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:9558800-9559200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
28	chr12:9558800-9559200	ZNF genes & repeats	Thymus	Thymus
29	chr12:9558800-9559400	Active TSS	Fetal Stomach	stomach
30	chr12:9558800-9559600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr12:9558800-9559600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:9558800-9559600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:9558800-9559600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr12:9558800-9559800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:9558800-9559800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:9558800-9559800	Active TSS	Brain Anterior Caudate	brain
37	chr12:9558800-9559800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:9558800-9560000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:9558800-9560000	Active TSS	Psoas Muscle	Psoas
40	chr12:9558800-9560200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:9558800-9560200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:9558800-9560200	Active TSS	Adipose Nuclei	Adipose
43	chr12:9558800-9566600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:9559000-9559200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
45	chr12:9559000-9559200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:9559000-9559200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr12:9559000-9559200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:9559000-9559400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr12:9559000-9559400	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr12:9559000-9559400	Active TSS	Placenta	Placenta

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