Variant report

Variant	esv3449168
Chromosome Location	chr11:60084417-60085198
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MS4A4A-1	chr11:60085057-60085061	XLOC_009141

Variant related genes	Relation type
VGLL3	miRNA target sites

Extended variants
information (count: 32 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs185433149	chr11:60084441-60084442	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs12225299	chr11:60084465-60084466	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs76386110	chr11:60084485-60084486	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs61900469	chr11:60084489-60084490	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs77962986	chr11:60084526-60084527	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs550818058	chr11:60084567-60084568	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs116462705	chr11:60084580-60084581	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs190194813	chr11:60084594-60084595	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs147517526	chr11:60084715-60084716	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs547626045	chr11:60084717-60084718	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs547227165	chr11:60084743-60084744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs182562931	chr11:60084775-60084776	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs535788915	chr11:60084792-60084793	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs554130873	chr11:60084817-60084818	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140285363	chr11:60084821-60084822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs539394089	chr11:60084826-60084827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs544327841	chr11:60084884-60084885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs187253324	chr11:60084891-60084892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs554640006	chr11:60084926-60084927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs549783913	chr11:60084928-60084929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs556786296	chr11:60084945-60084946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs115867664	chr11:60084980-60084981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs193019279	chr11:60085001-60085002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs10897030	chr11:60085012-60085013	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs113969821	chr11:60085022-60085023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs140106256	chr11:60085044-60085045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs542172875	chr11:60085077-60085078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs10897031	chr11:60085080-60085081	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs374039762	chr11:60085097-60085098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs530944408	chr11:60085099-60085100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs12277654	chr11:60085103-60085104	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs371195208	chr11:60085115-60085116	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Multiple myeloma	20724749	CNVD
Wilms tumour	21544195	CNVD
Autism	22495311	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-small cell lung cancer	21385341	CNVD
Intellectual disability	22102821	CNVD
Glioblastoma multiforme	21138945	CNVD
Esophageal cancer	21851588	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	21637783	CNVD
Acute myeloid leukemia	16864856	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21484798	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	21386901	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	20837533	CNVD
Breast cancer	21264507	CNVD
Cervical cancer	21063398	CNVD
Glioblastoma multiforme	19960244	CNVD
Liposarcoma	21253554	CNVD
Neuroblastoma	18923524	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Neuroblastoma	17533364	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Pituitary adenoma	18645599	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	21080181	CNVD
Smith-Lemli-Opitz syndrome	21572526	CNVD
Multiple myeloma	16461302	CNVD
Cancer	16751803	CNVD
Seminomas	18059402	CNVD
Autism	20808228	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Lung adenocarcinoma	17086460	CNVD
Metanephric adenoma	20802469	CNVD
Chordoma	21602918	CNVD
Melanoma	18172304	CNVD
Gastric cancer	16891809	CNVD
Lung cancer	17086460	CNVD
Chordoma	18071362	CNVD

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:60083800-60084600	Flanking Active TSS	GM12878-XiMat	blood
2	chr11:60083800-60086200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:60084400-60086400	Weak transcription	Placenta	Placenta
4	chr11:60084600-60084800	Enhancers	GM12878-XiMat	blood
5	chr11:60085000-60085800	Weak transcription	GM12878-XiMat	blood

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