Variant report

Variant	esv3414428
Chromosome Location	chr15:56363060-56366358
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr15:56363485-56363774	K562	blood:	n/a	n/a
2	CTCF	chr15:56363610-56363680	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:56364140-56364290	Hela-S3	cervix:	n/a	n/a
4	E2F4	chr15:56364952-56365145	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr15:56365700-56365703	GM12878	blood:	n/a	n/a
6	MYC	chr15:56363558-56363674	MCF-7	breast:	n/a	n/a
7	MYC	chr15:56363510-56363785	MCF-7	breast:	n/a	chr15:56363542-56363552
8	MYC	chr15:56364748-56365054	A549	lung:	n/a	n/a
9	MYC	chr15:56365702-56365744	K562	blood:	n/a	n/a
10	NFYB	chr15:56364202-56364461	Hela-S3	cervix:	n/a	n/a
11	NRF1	chr15:56364326-56364358	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:56363377-56363730	MCF-7	breast:	n/a	n/a
13	POLR2A	chr15:56364918-56365107	MCF-7	breast:	n/a	n/a
14	POLR2A	chr15:56364202-56364363	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr15:56365436-56366160	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr15:56365796-56366060	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:56365634-56365637	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:56363513-56363685	A549	lung:	n/a	n/a
19	POLR2A	chr15:56364840-56365231	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:56364768-56365109	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr15:56363640-56363684	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:56363305-56363816	MCF-7	breast:	n/a	n/a
23	POLR2A	chr15:56364913-56364916	MCF-7	breast:	n/a	n/a
24	POLR2A	chr15:56364197-56364485	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:56364154-56364350	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:56363576-56363715	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:56363597-56363684	A549	lung:	n/a	n/a
28	POLR2A	chr15:56364043-56364612	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:56365155-56365159	MCF-7	breast:	n/a	n/a
30	POLR2A	chr15:56363493-56363682	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr15:56363556-56363733	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr15:56363302-56363783	MCF-7	breast:	n/a	n/a
33	POLR2A	chr15:56364914-56364944	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr15:56364806-56366156	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr15:56364689-56365240	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:56365837-56366046	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr15:56363574-56363675	A549	lung:	n/a	n/a
38	POLR2A	chr15:56365593-56365629	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr15:56363594-56363688	A549	lung:	n/a	n/a
40	POLR2A	chr15:56365652-56365931	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr15:56364202-56364484	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr15:56363439-56363806	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr15:56364789-56365237	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr15:56363530-56363689	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:56363543-56363709	A549	lung:	n/a	n/a
46	SMC3	chr15:56364323-56364345	GM12878	blood:	n/a	n/a
47	TAF1	chr15:56363479-56363756	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF1	chr15:56363423-56363766	H1-hESC	embryonic stem cell:	n/a	n/a
49	TBP	chr15:56364940-56364988	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TEX9-2	chr15:56363619-56363837	NONHSAT044014
2	lnc-RFX7-2	chr15:56363458-56363839	l_1162_chr15:56293600-56416163_liver

No data

Variant related genes	Relation type
CD24P2	TF binding region

Extended variants
information (count: 222 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:222 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372850382	chr15:56363306-56363307	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs139026487	chr15:56363321-56363322	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs532998376	chr15:56363335-56363336	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs565701685	chr15:56363346-56363347	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs12442656	chr15:56363358-56363359	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs554617719	chr15:56363375-56363376	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs370401553	chr15:56363384-56363385	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs75810485	chr15:56363393-56363394	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs552029195	chr15:56363428-56363429	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs536807296	chr15:56363429-56363430	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs72736445	chr15:56363430-56363431	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs182403493	chr15:56363455-56363456	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs545727332	chr15:56363486-56363487	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs142387870	chr15:56363533-56363534	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs373808107	chr15:56363544-56363545	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs572377789	chr15:56363549-56363550	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs35722267	chr15:56363579-56363580	Inactive region	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs186738833	chr15:56363585-56363586	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs561391735	chr15:56363599-56363600	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs549902374	chr15:56363605-56363606	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs115263263	chr15:56363606-56363607	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs34777702	chr15:56363631-56363632	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs115113165	chr15:56363645-56363646	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs532837297	chr15:56363647-56363648	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs552930062	chr15:56363683-56363684	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs34979470	chr15:56363698-56363699	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs117251408	chr15:56363714-56363715	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs547881919	chr15:56363746-56363747	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs568147235	chr15:56363749-56363750	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs536790760	chr15:56363752-56363753	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs372284704	chr15:56363763-56363764	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs375320832	chr15:56363767-56363768	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs72736446	chr15:56363788-56363789	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs556723144	chr15:56363796-56363797	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs144767671	chr15:56363805-56363806	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs576656753	chr15:56363810-56363811	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs539271767	chr15:56363820-56363821	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs71441425	chr15:56363835-56363836	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs535901216	chr15:56363836-56363837	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs536741430	chr15:56363853-56363854	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs57099157	chr15:56363861-56363862	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs371991592	chr15:56363876-56363877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs562411362	chr15:56363881-56363882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs576526310	chr15:56364054-56364055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs553196483	chr15:56364068-56364069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs192567609	chr15:56364089-56364090	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs541368410	chr15:56364114-56364115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs539396020	chr15:56364129-56364130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs561171687	chr15:56364137-56364138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs72736447	chr15:56364157-56364158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	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
Melanoma	18172304	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
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	21129771	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Acute monocytic leukemia	16498392	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Gastric adenocarcinoma	19115996	CNVD
Congenital diaphragmatic hernia	21341218	CNVD
Holoprosencephaly	21359414	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56363600-56383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr15:56364800-56365200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr15:56364800-56365200	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr15:56364800-56365200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:56365000-56365200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr15:56365200-56365400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:56365400-56365600	Enhancers	Fetal Brain Male	brain
8	chr15:56365600-56366400	Weak transcription	Fetal Brain Male	brain

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