Variant report

Variant	esv3312139
Chromosome Location	chr15:30239460-30244058
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	chr15:30216407..30219283-chr15:30243845..30246238,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GOLGA8J-1	chr15:30241229-30241270	XLOC_011198
2	lnc-GOLGA8J-1	chr15:30240229-30241102	XLOC_011198

Variant related genes	Relation type
MGAT4A	miRNA target sites
MGEA5	miRNA target sites

Extended variants
information (count: 270 )
Associated
traits (count: 154 )

Variant overlapped rSNPs/rCNVs (count:270 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529614914	chr15:30239480-30239481	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs536049501	chr15:30239494-30239495	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs181866212	chr15:30239504-30239505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs187037234	chr15:30239535-30239536	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs531855542	chr15:30239544-30239545	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs544352193	chr15:30239580-30239581	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs189890275	chr15:30239582-30239583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs181940241	chr15:30239591-30239592	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs571291700	chr15:30239592-30239593	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs533851620	chr15:30239621-30239622	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs547013391	chr15:30239631-30239632	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs566877932	chr15:30239699-30239700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs575963110	chr15:30239721-30239722	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs543429085	chr15:30239722-30239723	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs561155375	chr15:30239797-30239798	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs143728143	chr15:30239820-30239821	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs144725942	chr15:30239833-30239834	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs575929270	chr15:30239836-30239837	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs368888212	chr15:30239894-30239895	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs11070176	chr15:30239907-30239908	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs376507452	chr15:30239925-30239926	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs186305281	chr15:30239985-30239986	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs148525806	chr15:30240032-30240033	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs540674956	chr15:30240055-30240056	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs560492642	chr15:30240089-30240090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs142179665	chr15:30240142-30240143	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs540794620	chr15:30240198-30240199	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs190010778	chr15:30240221-30240222	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs182290210	chr15:30240244-30240245	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs61441097	chr15:30240248-30240249	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs186482108	chr15:30240332-30240333	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs529878928	chr15:30240340-30240341	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs372880096	chr15:30240379-30240380	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs80302619	chr15:30240380-30240381	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs376150435	chr15:30240406-30240407	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs541582383	chr15:30240407-30240408	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs529110586	chr15:30240413-30240414	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs375939712	chr15:30240419-30240420	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs547052354	chr15:30240451-30240452	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs12905868	chr15:30240454-30240455	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs367928767	chr15:30240463-30240464	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs539671974	chr15:30240464-30240465	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs377061229	chr15:30240465-30240466	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs549345136	chr15:30240467-30240468	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs569886697	chr15:30240469-30240470	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs145294035	chr15:30240471-30240472	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs558475435	chr15:30240473-30240474	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs35983966	chr15:30240480-30240481	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs370236460	chr15:30240481-30240482	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs572164231	chr15:30240498-30240499	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:154)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
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
Prader-willi syndrome	21504564	CNVD
The inv dup or idic syndrome	19019226	CNVD
Prader-willi syndrome	21233802	CNVD
Angelman syndrome	16617304	CNVD
Angelman syndrome	20970697	CNVD
Autism	22958593	CNVD
Prader-willi syndrome	16617304	CNVD
Prader-willi syndrome	18923514	CNVD
Prader-willi syndrome	20970697	CNVD
Angelman syndrome	16183798	CNVD
Angelman syndrome	18923514	CNVD
Prader-willi syndrome	22241247	CNVD
Epilepsy	20970697	CNVD
Autism	20970697	CNVD
Autism	19935738	CNVD
Autism	22930557	CNVD
Autism	19966786	CNVD
Autism	18923514	CNVD
Autism	18925931	CNVD
Autism	18835857	CNVD
Prader-willi syndrome	18835857	CNVD
Prader-willi syndrome	22152151	CNVD
Autism	22241247	CNVD
15q-syndrome	21725066	CNVD
Prader-willi syndrome	21503198	CNVD
Autism	21956041	CNVD
Prader-willi syndrome	16760730	CNVD
Prader-willi syndrome	22470819	CNVD
prenatal diagnosis	20453657	CNVD
Prader-willi syndrome	17867985	CNVD
Angelman syndrome	21072004	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
Hodgkin''s lymphoma	18641027	CNVD
Prader-willi syndrome	18781185	CNVD
Melanoma	18172304	CNVD
Autism	17322880	CNVD
Prader-willi syndrome	19329560	CNVD
Autism	17999366	CNVD
Autism	17901113	CNVD
Neurodevelopmental disorder	17015230	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Mental retardation	18923513	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
Gastrointestinal stromal cancer	20818650	CNVD
Intellectual disability	22102821	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21509527	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
Schizophrenia	19197363	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Angelman syndrome	18787571	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Abnormal corpus callosum	21572526	CNVD
idiopathic generalized epilepsy	19843651	CNVD
Autism	20531469	CNVD
Neuropsychiatric disorder	20506139	CNVD
Austim spectrum disorder	21302340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Mental retardation	17124404	CNVD
Autism	19204725	CNVD
Schizophrenia	19204725	CNVD
Schizophrenia	19149910	CNVD
Schizophrenia	20967226	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Autism	19843651	CNVD
Schizophrenia	19843651	CNVD
Schizophrenia	23813976	CNVD
Cognitive impairment	21505072	CNVD
Autism	22543975	CNVD
small cell lung cancer	20016488	CNVD
Autism	22495309	CNVD
Schizophrenia	20388499	CNVD
Epilepsy	22499536	CNVD
Schizophrenia	22499536	CNVD
Schizophrenia	18923514	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20553308	CNVD
Schizophrenia	21956041	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Mental retardation	21956041	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Autism	21269290	CNVD
Intellectual disability	21269290	CNVD
Schizophrenia	21269290	CNVD
Colorectal cancer	21128281	CNVD
Epilepsy	19289393	CNVD
Epilepsy	20643615	CNVD
Mental retardation	19289393	CNVD
Mental retardation	20152051	CNVD
Schizophrenia	19289393	CNVD
dysmorphic features	19289393	CNVD
idiopathic epilepsies	19341504	CNVD
idiopathic generalized epilepsy	19592580	CNVD
idiopathic generalized epilepsy	19136953	CNVD
Autism	22094647	CNVD
Developmental delay	19898479	CNVD
Mental retardation	18278044	CNVD
Mental retardation	19898479	CNVD
Prader-willi syndrome	18854863	CNVD
Schizophrenia	19855392	CNVD
Ovarian cancer	22174824	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Attention deficit hyperactivity disorder	22420046	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Autism	21865298	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30232600-30260400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:30234200-30241200	Weak transcription	Right Atrium	heart
3	chr15:30237200-30239600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:30237200-30240000	Enhancers	Brain Angular Gyrus	brain
5	chr15:30237200-30240800	Enhancers	Brain Hippocampus Middle	brain
6	chr15:30237400-30240000	Enhancers	Brain Substantia Nigra	brain
7	chr15:30237600-30239800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:30237600-30240800	Enhancers	Brain Anterior Caudate	brain
9	chr15:30237600-30241000	Enhancers	Brain Cingulate Gyrus	brain
10	chr15:30238800-30242400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:30239200-30239600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:30239600-30240200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr15:30240000-30242400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:30240000-30242400	Weak transcription	Brain Substantia Nigra	brain
15	chr15:30240200-30242400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:30240200-30253800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:30240800-30242400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:30240800-30242600	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:30241000-30242400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:30241200-30241800	Strong transcription	Right Atrium	heart
21	chr15:30241400-30242800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:30241800-30244200	Weak transcription	Right Atrium	heart
23	chr15:30242400-30242600	Genic enhancers	Brain Anterior Caudate	brain
24	chr15:30242400-30242800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
25	chr15:30242400-30242800	Enhancers	Gastric	stomach
26	chr15:30242400-30242800	ZNF genes & repeats	Pancreas	Pancrea
27	chr15:30242400-30243200	Genic enhancers	Brain Angular Gyrus	brain
28	chr15:30242400-30243200	Genic enhancers	Brain Substantia Nigra	brain
29	chr15:30242400-30244600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:30242400-30244800	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:30242400-30245200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:30242600-30242800	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr15:30242600-30242800	Enhancers	Fetal Brain Male	brain
34	chr15:30242600-30243000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:30242600-30245400	Enhancers	Brain Hippocampus Middle	brain
36	chr15:30242800-30243200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:30242800-30243200	Weak transcription	Pancreas	Pancrea
38	chr15:30242800-30243800	Weak transcription	Brain Anterior Caudate	brain
39	chr15:30242800-30245400	Weak transcription	Gastric	stomach
40	chr15:30242800-30254200	Weak transcription	Fetal Brain Male	brain
41	chr15:30243000-30257800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:30243200-30243600	Weak transcription	Brain Substantia Nigra	brain
43	chr15:30243200-30243800	Weak transcription	Brain Angular Gyrus	brain
44	chr15:30243400-30246000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr15:30243600-30244200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:30243600-30245200	Enhancers	Brain Substantia Nigra	brain
47	chr15:30243600-30245400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:30243800-30244800	Enhancers	Brain Angular Gyrus	brain
49	chr15:30243800-30245200	Enhancers	Brain Anterior Caudate	brain

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