Variant report

Variant	esv3420287
Chromosome Location	chr5:115893903-115895001
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr5:115894735-115895142	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr5:115894910-115895174	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr5:115893294-115893914	SK-N-SH	brain:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
4	CTCF	chr5:115893231-115893961	A549	lung:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
5	CTCF	chr5:115894680-115894830	GM06990	blood:	n/a	n/a
6	ELF1	chr5:115894906-115895363	GM12878	blood:	n/a	n/a
7	JUND	chr5:115894957-115895105	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr5:115894797-115895296	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:115894958-115895282	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:115894489-115896585	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:115894781-115896063	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:115894807-115895947	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr5:115893243-115893911	A549	lung:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
14	RAD21	chr5:115893234-115893909	HCT-116	colon:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
15	SIN3A	chr5:115894845-115895458	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr5:115894892-115895199	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr5:115894860-115895251	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP1	chr5:115894875-115895305	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAL1	chr5:115894944-115895099	K562	blood:	n/a	n/a
20	TBP	chr5:115894930-115895247	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr5:115894868-115895213	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF12	chr5:115894830-115895242	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr5:115894905-115895410	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr5:115894863-115895881	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115895001..115897524-chr5:115899186..115901085,2	K562	blood:
2	chr5:115892597..115894869-chr5:115895299..115897417,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region
ENSG00000239528	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs369531944	chr5:115893913-115893914	Enhancers Weak transcription Genic enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs559942934	chr5:115893998-115893999	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs190116544	chr5:115894008-115894009	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs570459580	chr5:115894019-115894020	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530318844	chr5:115894046-115894047	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539607101	chr5:115894082-115894083	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs200809850	chr5:115894149-115894150	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs375971715	chr5:115894150-115894151	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs369006905	chr5:115894151-115894152	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs12658703	chr5:115894220-115894221	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs569922940	chr5:115894221-115894222	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs566749337	chr5:115894271-115894272	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs1700486	chr5:115894438-115894439	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs181708865	chr5:115894451-115894452	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs377100610	chr5:115894454-115894455	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs369614232	chr5:115894455-115894456	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs372734789	chr5:115894456-115894457	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs199824220	chr5:115894457-115894458	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs578155629	chr5:115894493-115894494	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs545993283	chr5:115894539-115894540	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
21	rs254210	chr5:115894566-115894567	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs254209	chr5:115894579-115894580	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs542100743	chr5:115894588-115894589	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
24	rs147896492	chr5:115894595-115894596	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
25	rs530481002	chr5:115894652-115894653	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
26	rs550318169	chr5:115894663-115894664	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
27	rs570181915	chr5:115894700-115894701	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
28	rs141563898	chr5:115894702-115894703	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
29	rs570617185	chr5:115894737-115894738	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
30	rs566712570	chr5:115894769-115894770	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
31	rs535720271	chr5:115894791-115894792	Flanking Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
32	rs185971882	chr5:115894853-115894854	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
33	rs555978573	chr5:115894894-115894895	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
34	rs254208	chr5:115894895-115894896	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs189526476	chr5:115894925-115894926	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
36	rs147026341	chr5:115894961-115894962	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
37	rs532307799	chr5:115894975-115894976	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
38	rs574612339	chr5:115894976-115894977	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
39	rs147745400	chr5:115894995-115894996	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
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
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
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	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
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
Colorectal cancer	16272173	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Ovarian cancer	21720365	CNVD
Salivary gland tumor	18059337	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	19377443	CNVD
Prostate cancer	16461572	CNVD
Myelofibrosis	22110671	CNVD
Sezary syndrome	18413736	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Glaucoma	21310917	CNVD
Glioblastoma multiforme	22286061	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Prostate cancer	22341455	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
2	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:115885400-115894000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:115885400-115894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
6	chr5:115887400-115895000	Weak transcription	Lung	lung
7	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
8	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:115889400-115895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
12	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
14	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
15	chr5:115890800-115894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:115890800-115894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115890800-115894800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:115890800-115895000	Weak transcription	Left Ventricle	heart
19	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
20	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
23	chr5:115891000-115894200	Enhancers	Brain Anterior Caudate	brain
24	chr5:115891000-115894600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:115891000-115894600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:115891000-115894600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
29	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:115891000-115907600	Weak transcription	Ovary	ovary
31	chr5:115891200-115904600	Weak transcription	Fetal Stomach	stomach
32	chr5:115891400-115895400	Weak transcription	Psoas Muscle	Psoas
33	chr5:115891400-115905200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:115891800-115894600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:115891800-115894800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:115892000-115894800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:115892600-115894400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:115892600-115894800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:115893000-115894800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:115893000-115894800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:115893000-115894800	Weak transcription	Fetal Intestine Small	intestine
42	chr5:115893200-115894400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:115893200-115894800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr5:115893200-115895000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:115893200-115895200	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:115893200-115895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:115893400-115894600	Weak transcription	Brain Angular Gyrus	brain
48	chr5:115893400-115895000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr5:115893400-115895600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:115893600-115894400	Weak transcription	Brain Substantia Nigra	brain

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