Variant report

Variant	nsv593773
Chromosome Location	chr4:16227594-16228293
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:274)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:274 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr4:16228090-16228399	K562	blood:	n/a	chr4:16228224-16228238
2	ATF3	chr4:16228128-16228317	HepG2	liver:	n/a	chr4:16228228-16228238
3	ATF3	chr4:16228068-16228394	K562	blood:	n/a	chr4:16228228-16228238
4	BHLHE40	chr4:16227317-16227722	GM12878	blood:	n/a	n/a
5	BHLHE40	chr4:16227421-16227688	K562	blood:	n/a	n/a
6	BHLHE40	chr4:16227939-16228356	K562	blood:	n/a	n/a
7	BHLHE40	chr4:16228156-16228409	GM12878	blood:	n/a	n/a
8	CCNT2	chr4:16227278-16229113	K562	blood:	n/a	chr4:16227795-16227804 chr4:16228813-16228822 chr4:16228154-16228163
9	CEBPB	chr4:16227469-16228056	Hela-S3	cervix:	n/a	n/a
10	CEBPD	chr4:16228183-16228571	HepG2	liver:	n/a	n/a
11	CHD1	chr4:16226879-16227693	GM12878	blood:	n/a	n/a
12	CHD1	chr4:16227900-16229043	GM12878	blood:	n/a	chr4:16228147-16228157 chr4:16228152-16228162
13	CHD2	chr4:16228217-16228364	Hela-S3	cervix:	n/a	n/a
14	CHD2	chr4:16228211-16228411	GM12878	blood:	n/a	n/a
15	CHD2	chr4:16227751-16227906	GM12878	blood:	n/a	n/a
16	CREB1	chr4:16227920-16228543	K562	blood:	n/a	n/a
17	CREB1	chr4:16228147-16228410	A549	lung:	n/a	n/a
18	CREB1	chr4:16227904-16228545	GM12878	blood:	n/a	n/a
19	CREB1	chr4:16227828-16228594	HepG2	liver:	n/a	n/a
20	CREB1	chr4:16227976-16228470	H1-hESC	embryonic stem cell:	n/a	n/a
21	CREB1	chr4:16228015-16228541	A549	lung:	n/a	n/a
22	CREB1	chr4:16227956-16228467	HepG2	liver:	n/a	n/a
23	CREB1	chr4:16227973-16228511	GM12878	blood:	n/a	n/a
24	CREB1	chr4:16228026-16228388	ECC-1	luminal epithelium:	n/a	n/a
25	CREB1	chr4:16227983-16228525	H1-hESC	embryonic stem cell:	n/a	n/a
26	CREB1	chr4:16227972-16228511	K562	blood:	n/a	n/a
27	CREB1	chr4:16228140-16228339	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr4:16227720-16227870	GM12874	blood:	n/a	n/a
29	E2F6	chr4:16227576-16228466	K562	blood:	n/a	chr4:16228102-16228111 chr4:16227816-16227825
30	E2F6	chr4:16228010-16228516	K562	blood:	n/a	chr4:16228102-16228111
31	E2F6	chr4:16228145-16228311	K562	blood:	n/a	n/a
32	ELF1	chr4:16228024-16228650	K562	blood:	n/a	n/a
33	ELF1	chr4:16228075-16229485	GM12878	blood:	n/a	n/a
34	ELF1	chr4:16228147-16228433	K562	blood:	n/a	n/a
35	ELF1	chr4:16227874-16228584	GM12878	blood:	n/a	n/a
36	EP300	chr4:16227921-16228628	ECC-1	luminal epithelium:	n/a	n/a
37	EP300	chr4:16227366-16227720	GM12878	blood:	n/a	n/a
38	EP300	chr4:16228193-16228305	K562	blood:	n/a	n/a
39	EP300	chr4:16227607-16227642	K562	blood:	n/a	n/a
40	ETS1	chr4:16227820-16228550	K562	blood:	n/a	chr4:16228102-16228113
41	ETS1	chr4:16227401-16227778	K562	blood:	n/a	n/a
42	GTF2F1	chr4:16228256-16228400	K562	blood:	n/a	n/a
43	HA-E2F1	chr4:16227491-16228928	Hela-S3	cervix:	n/a	chr4:16228102-16228111 chr4:16227816-16227825
44	HA-E2F1	chr4:16227309-16227939	MCF-7	breast:	n/a	chr4:16227816-16227825
45	HCFC1	chr4:16227898-16228947	K562	blood:	n/a	n/a
46	HCFC1	chr4:16226663-16228826	Hela-S3	cervix:	n/a	n/a
47	HCFC1	chr4:16227577-16227692	K562	blood:	n/a	n/a
48	HEY1	chr4:16228156-16228428	HepG2	liver:	n/a	n/a
49	HEY1	chr4:16227828-16228148	K562	blood:	n/a	n/a
50	HEY1	chr4:16228187-16228443	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:16228062-16228112	SAEC	small airway:	n/a
2	chr4:16227813-16227863	HUVEC	blood vessel:	n/a
3	chr4:16228062-16228112	IMR90	lung:	fetal
4	chr4:16228062-16228112	AG09319	gingival:	n/a
5	chr4:16228062-16228112	HRE	kidney:	n/a
6	chr4:16228062-16228112	SK-N-SH	brain:	n/a
7	chr4:16227813-16227863	AG04449	skin:	fetal
8	chr4:16228062-16228112	PrEC	prostate:	n/a
9	chr4:16228062-16228112	A549	lung:	n/a
10	chr4:16228062-16228112	HCF	heart:	n/a
11	chr4:16227813-16227863	GM12892	blood:	n/a
12	chr4:16228062-16228112	AG04450	lung:	fetal
13	chr4:16227813-16227863	HCPEpiC	choroid plexus:	n/a
14	chr4:16227813-16227863	MCF-7	breast:	n/a
15	chr4:16227813-16227863	NHDF-neo	bronchial:	n/a
16	chr4:16227813-16227863	A549	lung:	n/a
17	chr4:16227813-16227863	K562	blood:	n/a
18	chr4:16228062-16228112	HEEpiC	esophagus:	n/a
19	chr4:16228062-16228112	GM19239	blood:	n/a
20	chr4:16227813-16227863	LNCaP	prostate:	n/a
21	chr4:16228062-16228112	NT2-D1	testis:	n/a
22	chr4:16227813-16227863	ECC-1	luminal epithelium:	n/a
23	chr4:16227813-16227863	HL-60	blood:	n/a
24	chr4:16227813-16227863	GM12891	blood:	n/a
25	chr4:16227813-16227863	HEK293	kidney:	embryo
26	chr4:16227813-16227863	SKMC	muscle:	n/a
27	chr4:16228062-16228112	SKMC	muscle:	n/a
28	chr4:16228062-16228112	HMEC	breast:	n/a
29	chr4:16227813-16227863	NHBE	bronchial:	n/a
30	chr4:16227813-16227863	AG10803	skin:	n/a
31	chr4:16227813-16227863	AG09309	skin:	n/a
32	chr4:16228062-16228112	AoSMC	blood vessel:	n/a
33	chr4:16228062-16228112	HEK293	kidney:	embryo
34	chr4:16227813-16227863	AG04450	lung:	fetal
35	chr4:16227813-16227863	NH-A	brain:	n/a
36	chr4:16228062-16228112	HRPEpiC	eye:	n/a
37	chr4:16227813-16227863	BJ	skin:	n/a
38	chr4:16228062-16228112	MCF10A-Er-Src	breast:	n/a
39	chr4:16228062-16228112	Hepatocyte	liver:	n/a
40	chr4:16228062-16228112	ECC-1	luminal epithelium:	n/a
41	chr4:16228062-16228112	HUVEC	blood vessel:	n/a
42	chr4:16227813-16227863	BE2_C	brain:	n/a
43	chr4:16228062-16228112	Caco-2	colon:	n/a
44	chr4:16228062-16228112	GM12891	blood:	n/a
45	chr4:16228062-16228112	AG10803	skin:	n/a
46	chr4:16228062-16228112	LNCaP	prostate:	n/a
47	chr4:16227813-16227863	SAEC	small airway:	n/a
48	chr4:16228062-16228112	NHBE	bronchial:	n/a
49	chr4:16227813-16227863	U87	brain:	n/a
50	chr4:16227813-16227863	Caco-2	colon:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:16216932..16218804-chr4:16227245..16229857,2	MCF-7	breast:
2	chr17:59476916..59479068-chr4:16227271..16228837,2	MCF-7	breast:
3	chr21:33104183..33104701-chr4:16227636..16228281,2	Hela-S3	cervix:
4	chr4:15002785..15006911-chr4:16226901..16230678,5	K562	blood:
5	chr4:16227890..16229761-chr4:17577650..17579806,2	MCF-7	breast:
6	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
7	chr4:15681714..15684664-chr4:16226494..16229781,3	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD38-2	chr4:16228286-16230207	ENSG00000263327.2
2	lnc-CD38-2	chr4:16228286-16228800	ENSG00000225917
3	lnc-CD38-2	chr4:16228286-16228800	NONHSAT095674

No data

Variant related genes	Relation type
TAPT1-AS1	TF binding region
TAPT1	TF binding region
TAPT1-AS1	CpG island
TAPT1	CpG island
ENSG00000137449	chromatin interactions
ENSG00000267280	chromatin interactions
ENSG00000156304	chromatin interactions
ENSG00000237765	chromatin interactions
ENSG00000247624	chromatin interactions
ENSG00000121068	chromatin interactions
ENSG00000118564	chromatin interactions
ENSG00000267131	chromatin interactions
ENSG00000002549	chromatin interactions
ENSG00000169762	chromatin interactions
PDGFRA	miRNA target sites

Extended variants
information (count: 20 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6812660	chr4:16227594-16227595	Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs369738317	chr4:16227624-16227625	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
3	rs573445732	chr4:16227640-16227641	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
4	rs370126610	chr4:16227642-16227643	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
5	rs564253781	chr4:16227648-16227649	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
6	rs576219410	chr4:16227664-16227665	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
7	rs533189278	chr4:16227682-16227683	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
8	rs546542346	chr4:16227685-16227686	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
9	rs547336789	chr4:16227719-16227720	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
10	rs566779514	chr4:16227779-16227780	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
11	rs535058605	chr4:16227780-16227781	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
12	rs3749543	chr4:16227781-16227782	Active TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs3749544	chr4:16227823-16227824	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs567614266	chr4:16227872-16227873	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
15	rs28384238	chr4:16227944-16227945	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
16	rs551534255	chr4:16228176-16228177	Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
17	rs557457554	chr4:16228189-16228190	Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
18	rs577006870	chr4:16228208-16228209	Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
19	rs12643453	chr4:16228250-16228251	Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
20	rs554214258	chr4:16228269-16228270	Active TSS Weak transcription	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:147 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16224800-16227600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr4:16225600-16227600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr4:16225600-16230800	Active TSS	A549	lung
4	chr4:16225800-16227600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:16225800-16230000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:16226000-16227600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr4:16226200-16227600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:16226200-16227600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:16226200-16229600	Active TSS	Right Atrium	heart
10	chr4:16226400-16228400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:16226400-16228800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr4:16226400-16228800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:16226400-16228800	Active TSS	Fetal Thymus	thymus
14	chr4:16226400-16228800	Active TSS	Thymus	Thymus
15	chr4:16226400-16229000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:16226400-16229200	Active TSS	Fetal Stomach	stomach
17	chr4:16226400-16229400	Active TSS	Aorta	Aorta
18	chr4:16226400-16229400	Active TSS	HepG2	liver
19	chr4:16226400-16229600	Active TSS	Left Ventricle	heart
20	chr4:16226400-16229600	Active TSS	Psoas Muscle	Psoas
21	chr4:16226400-16229800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:16226400-16229800	Active TSS	Right Ventricle	heart
23	chr4:16226400-16229800	Active TSS	Stomach Smooth Muscle	stomach
24	chr4:16226400-16230600	Active TSS	GM12878-XiMat	blood
25	chr4:16226600-16228600	Active TSS	Fetal Muscle Leg	muscle
26	chr4:16226600-16228800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:16226600-16228800	Active TSS	NH-A	brain
28	chr4:16226600-16229000	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr4:16226600-16229200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:16226600-16229200	Active TSS	Fetal Intestine Small	intestine
31	chr4:16226600-16229400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:16226600-16229400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr4:16226600-16229400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:16226600-16229400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr4:16226600-16229600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:16226600-16229600	Active TSS	HMEC	breast
37	chr4:16226600-16229800	Active TSS	H1 Cell Line	embryonic stem cell
38	chr4:16226600-16229800	Active TSS	NHDF-Ad	bronchial
39	chr4:16226600-16230000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr4:16226600-16230800	Active TSS	K562	blood
41	chr4:16226800-16227600	Active TSS	Fetal Brain Male	brain
42	chr4:16226800-16227600	Flanking Active TSS	HUVEC	blood vessel
43	chr4:16226800-16227800	Active TSS	Fetal Lung	lung
44	chr4:16226800-16228600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:16226800-16228800	Active TSS	Fetal Muscle Trunk	muscle
46	chr4:16226800-16229000	Active TSS	HSMM	muscle
47	chr4:16226800-16229200	Active TSS	NHLF	lung
48	chr4:16226800-16229400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:16226800-16229400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:16226800-16229600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links