Variant report

Variant	esv3395475
Chromosome Location	chr4:559894-562779
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:560744..563501-chr4:564361..568313,3	K562	blood:
2	chr4:560447..562765-chr4:571972..574666,2	MCF-7	breast:
3	chr4:560309..561984-chr4:571273..573145,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGG-1	chr4:562509-568807	l_2577_chr4:560751-568807_brain
2	lnc-PIGG-1	chr4:560752-561223	l_2577_chr4:560751-568807_brain

Variant related genes	Relation type
ENSG00000273238	chromatin interactions

Extended variants
information (count: 73 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:73 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs576822966	chr4:560749-560750	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs189190394	chr4:560797-560798	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs182387274	chr4:560829-560830	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs142349888	chr4:560830-560831	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs114503376	chr4:560842-560843	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs73074224	chr4:560897-560898	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs527524852	chr4:560903-560904	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs78233832	chr4:560926-560927	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
9	rs564422059	chr4:560936-560937	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs531287709	chr4:560947-560948	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs549814352	chr4:561061-561062	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs568030644	chr4:561068-561069	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs73219270	chr4:561121-561122	Inactive region	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs187385673	chr4:561220-561221	ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs536606083	chr4:561221-561222	ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs146161359	chr4:561307-561308	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs534169388	chr4:561312-561313	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs375564293	chr4:561418-561419	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs558778886	chr4:561443-561444	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs386670404	chr4:561466-561467	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs114710984	chr4:561468-561469	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs370129749	chr4:561495-561496	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs537812484	chr4:561496-561497	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs556541580	chr4:561504-561505	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs190447158	chr4:561505-561506	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs116960925	chr4:561529-561530	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs79091673	chr4:561551-561552	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs368688454	chr4:561577-561578	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs572205014	chr4:561591-561592	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs576428011	chr4:561594-561595	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs546025917	chr4:561606-561607	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs564333681	chr4:561615-561616	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs12639825	chr4:561628-561629	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs7655590	chr4:561631-561632	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs141530096	chr4:561691-561692	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs78711764	chr4:561705-561706	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs547873645	chr4:561708-561709	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs150870257	chr4:561726-561727	Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs547465117	chr4:561891-561892	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs372723940	chr4:561968-561969	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs139306901	chr4:561988-561989	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs368432603	chr4:561995-561996	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs552368052	chr4:562028-562029	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs35839284	chr4:562043-562044	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs558986375	chr4:562102-562103	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs538125844	chr4:562139-562140	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs534775476	chr4:562154-562155	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs181638852	chr4:562158-562159	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs535528970	chr4:562191-562192	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs33972056	chr4:562200-562201	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:561200-561800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:561600-562200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:561800-562200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:562200-563800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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