Variant report

Variant	esv3496169
Chromosome Location	chr5:99853903-99857001
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	chr5:99852863..99854851-chr5:99869315..99872165,2	MCF-7	breast:
2	chr5:99840638..99843580-chr5:99851710..99854340,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST8SIA4-3	chr5:99854234-99854315	ENSG00000247877
2	lnc-ST8SIA4-3	chr5:99854234-99854315	ENSG00000247877
3	lnc-ST8SIA4-3	chr5:99854234-99854315	NONHSAT103002

Variant related genes	Relation type
ENSG00000174132	chromatin interactions
ENSG00000247877	chromatin interactions
TTLL12	miRNA target sites
HSPC159	miRNA target sites

Extended variants
information (count: 40 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139499989	chr5:99853915-99853916	Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs186143102	chr5:99853916-99853917	Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs192048462	chr5:99853938-99853939	Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs578218430	chr5:99853973-99853974	Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs545257757	chr5:99854011-99854012	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs529025055	chr5:99854012-99854013	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs563949076	chr5:99854060-99854061	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs369844281	chr5:99854082-99854083	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs144183947	chr5:99854093-99854094	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs115694564	chr5:99854111-99854112	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs560826159	chr5:99854116-99854117	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs528107769	chr5:99854191-99854192	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs6870025	chr5:99854269-99854270	ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs530695870	chr5:99854270-99854271	ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs571427756	chr5:99854305-99854306	ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs149151670	chr5:99854378-99854379	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs142353117	chr5:99854379-99854380	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs568755693	chr5:99854408-99854409	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs182987630	chr5:99854445-99854446	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs150980818	chr5:99854466-99854467	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs555459133	chr5:99854484-99854485	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs552085863	chr5:99854533-99854534	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs539591858	chr5:99854548-99854549	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs549730367	chr5:99854567-99854568	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs567295951	chr5:99854571-99854572	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs534677690	chr5:99854583-99854584	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs186691240	chr5:99854623-99854624	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs553367919	chr5:99854635-99854636	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs578180577	chr5:99854657-99854658	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs75247821	chr5:99854670-99854671	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs190725172	chr5:99854748-99854749	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs566139995	chr5:99854775-99854776	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs555693187	chr5:99856828-99856829	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs552951247	chr5:99856858-99856859	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs574104546	chr5:99856860-99856861	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs369760413	chr5:99856908-99856909	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs182124494	chr5:99856918-99856919	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs113947181	chr5:99856930-99856931	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs554056028	chr5:99856952-99856953	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs186235018	chr5:99856975-99856976	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
Non-small cell lung cancer	21829676	CNVD
adenomatous polyposis	22470819	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Urothelial carcinoma	21177765	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
Lung cancer	18438408	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	CNVD
Merkel cell carcinoma	19020549	CNVD
Squamous cell cancer	20885788	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17133270	CNVD
Acute myeloid leukemia	20729466	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
lymphocytic leukemia	21291569	CNVD
Testicular cancer	18059402	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16573809	CNVD
Renal cell carcinoma	18194544	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
abnormal development	18461090	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Ovarian cancer	21720365	CNVD
Prostate cancer	16461572	CNVD
Neurocytoma	17123091	CNVD
Salivary gland tumor	18059337	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Schizophrenia	23813976	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99852200-99854000	Enhancers	Esophagus	oesophagus
2	chr5:99852200-99854800	ZNF genes & repeats	GM12878-XiMat	blood
3	chr5:99853800-99854200	ZNF genes & repeats	Fetal Muscle Leg	muscle
4	chr5:99856800-99857000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:99857000-99857600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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