Variant report

Variant	nsv1028993
Chromosome Location	chr5:115523717-115563533
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	CTCF	chr5:115545600-115545750	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr5:115563372-115563423	GM13976	blood:	n/a	n/a
3	CTCF	chr5:115526780-115526930	HepG2	liver:	n/a	n/a
4	CTCF	chr5:115546959-115547004	Spleen_OC	spleen:	n/a	n/a
5	CTCF	chr5:115527000-115527150	GM06990	blood:	n/a	n/a
6	EBF1	chr5:115553101-115553358	GM12878	blood:	n/a	n/a
7	EP300	chr5:115562218-115562251	K562	blood:	n/a	n/a
8	FOXA1	chr5:115546868-115547069	T-47D	breast:	n/a	n/a
9	FOXA2	chr5:115546874-115547055	HepG2	liver:	n/a	n/a
10	GATA3	chr5:115562600-115562894	SH-SY5Y	brain:	n/a	n/a
11	GATA3	chr5:115532827-115533270	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr5:115555733-115556106	SH-SY5Y	brain:	n/a	n/a
13	GATA3	chr5:115540807-115540886	SH-SY5Y	brain:	n/a	n/a
14	GATA3	chr5:115532851-115533266	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr5:115532809-115533271	MCF-7	breast:	n/a	n/a
16	GTF2F1	chr5:115527179-115527209	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUN	chr5:115560931-115560946	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUN	chr5:115541691-115541827	HepG2	liver:	n/a	chr5:115541725-115541738
19	JUND	chr5:115554589-115554765	HepG2	liver:	n/a	n/a
20	KAP1	chr5:115544780-115545020	K562	blood:	n/a	n/a
21	MAFK	chr5:115546142-115546411	HepG2	liver:	n/a	chr5:115546288-115546299 chr5:115546284-115546300 chr5:115546287-115546301 chr5:115546289-115546300 chr5:115546288-115546299 chr5:115546289-115546300
22	MAFK	chr5:115555495-115555627	HepG2	liver:	n/a	n/a
23	MAFK	chr5:115546140-115546435	IMR90	lung:	n/a	chr5:115546288-115546299 chr5:115546284-115546300 chr5:115546287-115546301 chr5:115546289-115546300 chr5:115546288-115546299 chr5:115546289-115546300
24	MYC	chr5:115548513-115548606	H1-hESC	embryonic stem cell:	n/a	chr5:115548588-115548599 chr5:115548588-115548599
25	NFYA	chr5:115547516-115547716	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:115544329-115544356	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr5:115527331-115527464	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:115529090-115529122	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:115525744-115525813	ProgFib	skin:	n/a	n/a
30	POLR2A	chr5:115553932-115554011	MCF-7	breast:	n/a	n/a
31	POLR2A	chr5:115524379-115524454	Gliobla	brain:	n/a	n/a
32	POLR2A	chr5:115548793-115548814	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr5:115542870-115543154	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr5:115529315-115529431	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:115557721-115557727	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:115533530-115533551	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr5:115534330-115534480	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr5:115551954-115551970	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr5:115555976-115556087	MCF10A-Er-Src	breast:	n/a	n/a
40	ZNF384	chr5:115562075-115562105	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:
2	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-3	chr5:115549572-115550152	NONHSAT103355
2	lnc-SEMA6A-7	chr5:115553723-115553992	NONHSAT103356

Variant related genes	Relation type
HMGN2P27	TF binding region
RNU6-644P	TF binding region
ENSG00000232916	chromatin interactions
ENSG00000212457	chromatin interactions

Extended variants
information (count: 2054 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:2054 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs191622890	chr5:115523738-115523739	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs182966307	chr5:115523804-115523805	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs12522441	chr5:115523805-115523806	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs572330472	chr5:115523883-115523884	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs79848070	chr5:115523956-115523957	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs370144347	chr5:115523990-115523991	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs145111303	chr5:115523991-115523992	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs12522977	chr5:115524032-115524033	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs543639825	chr5:115524134-115524135	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs77256771	chr5:115524151-115524152	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs563776976	chr5:115524152-115524153	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs398093682	chr5:115524158-115524159	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs532610131	chr5:115524198-115524199	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs187367904	chr5:115524215-115524216	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs559460075	chr5:115524252-115524253	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs565755492	chr5:115524270-115524271	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs368639941	chr5:115524284-115524285	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs528464473	chr5:115524288-115524289	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs548633101	chr5:115524291-115524292	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs140551834	chr5:115524299-115524300	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs367878134	chr5:115524300-115524301	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs568401835	chr5:115524315-115524316	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs537292534	chr5:115524330-115524331	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs572956691	chr5:115524336-115524337	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs201344486	chr5:115524337-115524338	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs190378515	chr5:115524355-115524356	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs73257238	chr5:115524390-115524391	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs538329253	chr5:115524394-115524395	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs547181673	chr5:115524395-115524396	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs558600788	chr5:115524398-115524399	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs571983312	chr5:115524409-115524410	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs534601681	chr5:115524411-115524412	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs147598453	chr5:115524420-115524421	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs538076034	chr5:115524430-115524431	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs7717931	chr5:115524451-115524452	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs563436462	chr5:115524454-115524455	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs7718069	chr5:115524492-115524493	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs10042964	chr5:115524497-115524498	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs36100988	chr5:115524511-115524512	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs370136622	chr5:115524537-115524538	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs145463326	chr5:115524545-115524546	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs7718483	chr5:115524566-115524567	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs567337344	chr5:115524585-115524586	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs548557618	chr5:115524643-115524644	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs73257243	chr5:115524657-115524658	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs148892732	chr5:115524666-115524667	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs371897519	chr5:115524686-115524687	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs7718502	chr5:115524697-115524698	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs550786000	chr5:115524745-115524746	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs143611458	chr5:115524753-115524754	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:75)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD

Chromatin state (count:197 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115481400-115536000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:115489200-115526800	Weak transcription	Pancreas	Pancrea
3	chr5:115489800-115528600	Weak transcription	Ovary	ovary
4	chr5:115490000-115524400	Weak transcription	Left Ventricle	heart
5	chr5:115495200-115524400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:115497400-115528800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:115499200-115527400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:115502400-115524400	Weak transcription	Fetal Intestine Large	intestine
9	chr5:115502400-115526400	Weak transcription	Lung	lung
10	chr5:115508800-115529200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:115509200-115528400	Weak transcription	A549	lung
12	chr5:115509600-115533400	Weak transcription	HSMM	muscle
13	chr5:115510400-115524600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:115510400-115526200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:115510400-115526800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:115511800-115533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:115512000-115529200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:115512200-115526800	Weak transcription	Fetal Intestine Small	intestine
19	chr5:115517400-115526800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:115518200-115529000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:115518400-115524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:115518800-115529400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:115518800-115529800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:115518800-115548000	Weak transcription	Psoas Muscle	Psoas
25	chr5:115519800-115524400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:115520200-115526400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:115520400-115524800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:115520400-115528800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:115520800-115524200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:115520800-115524400	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:115520800-115527000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:115521000-115524400	Weak transcription	Aorta	Aorta
33	chr5:115521000-115526800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:115521000-115529400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:115521200-115530000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:115521400-115528800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:115521600-115527600	Strong transcription	Primary T cells from cord blood	blood
38	chr5:115522000-115523800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:115522000-115526400	Weak transcription	Liver	Liver
40	chr5:115522200-115536000	Weak transcription	Primary B cells from cord blood	blood
41	chr5:115522400-115524600	Weak transcription	Adipose Nuclei	Adipose
42	chr5:115522400-115528000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:115522400-115538000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:115522600-115526200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:115522600-115526600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:115522600-115526800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:115522600-115536800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:115522600-115540200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:115523000-115526200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:115523000-115527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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