Variant report

Variant	nsv549562
Chromosome Location	chr1:247279549-247283320
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	chr1:247282166-247282519	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr1:247282209-247282493	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr1:247282190-247282604	HepG2	liver:	n/a	n/a
4	CBX3	chr1:247279956-247280480	K562	blood:	n/a	n/a
5	CBX3	chr1:247279022-247279825	K562	blood:	n/a	n/a
6	CBX3	chr1:247278814-247282541	K562	blood:	n/a	n/a
7	CBX3	chr1:247280516-247280801	K562	blood:	n/a	n/a
8	CBX3	chr1:247280963-247282452	K562	blood:	n/a	n/a
9	CHD2	chr1:247282281-247282544	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:247282280-247282430	HCM	heart:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
11	CTCF	chr1:247282280-247282430	HUVEC	blood vessel:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
12	CTCF	chr1:247282260-247282530	HFF-Myc	foreskin:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
13	CTCF	chr1:247282320-247282470	GM12873	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
14	CTCF	chr1:247282294-247282448	Medullo	brain:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
15	CTCF	chr1:247282300-247282450	HCFaa	heart:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
16	CTCF	chr1:247282235-247282537	MCF-7	breast:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
17	CTCF	chr1:247282280-247282430	AG04450	lung:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
18	CTCF	chr1:247282270-247282463	NHEK	skin:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
19	CTCF	chr1:247282340-247282490	HEEpiC	esophagus:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
20	CTCF	chr1:247282360-247282510	HRPEpiC	eye:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
21	CTCF	chr1:247282260-247282410	GM12864	blood:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
22	CTCF	chr1:247282300-247282450	HFF-Myc	foreskin:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
23	CTCF	chr1:247282317-247282406	MCF-7	breast:	n/a	n/a
24	CTCF	chr1:247282320-247282470	GM12864	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
25	CTCF	chr1:247282280-247282430	HMEC	breast:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
26	CTCF	chr1:247282224-247282515	GM12892	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
27	CTCF	chr1:247282257-247282513	HepG2	liver:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
28	CTCF	chr1:247282320-247282470	AoAF	blood vessel:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
29	CTCF	chr1:247282300-247282450	HRE	kidney:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
30	CTCF	chr1:247282300-247282450	SAEC	small airway:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
31	CTCF	chr1:247282460-247282610	HCM	heart:	n/a	n/a
32	CTCF	chr1:247282210-247282590	HCT-116	colon:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
33	CTCF	chr1:247282300-247282450	HPF	lung:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
34	CTCF	chr1:247282246-247282498	GM19238	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
35	CTCF	chr1:247282204-247282504	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
36	CTCF	chr1:247282209-247282501	HepG2	liver:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
37	CTCF	chr1:247282280-247282430	AG09309	skin:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
38	CTCF	chr1:247282184-247282780	SK-N-SH	brain:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282711-247282724 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282664-247282673 chr1:247282314-247282327
39	CTCF	chr1:247282400-247282550	GM12869	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
40	CTCF	chr1:247282360-247282510	HFF	foreskin:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
41	CTCF	chr1:247282300-247282450	GM12872	blood:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
42	CTCF	chr1:247282340-247282490	GM12866	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
43	CTCF	chr1:247282380-247282530	GM12865	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
44	CTCF	chr1:247282231-247282648	MCF-7	breast:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
45	CTCF	chr1:247282307-247282472	GM10266	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
46	CTCF	chr1:247282300-247282450	GM12873	blood:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
47	CTCF	chr1:247282154-247282523	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
48	CTCF	chr1:247282367-247282448	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:247282420-247282570	GM12865	blood:	n/a	chr1:247282440-247282461 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456
50	CTCF	chr1:247282300-247282450	HPAF	blood vessel:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247282458-247282508	SKMC	muscle:	n/a
2	chr1:247282458-247282508	SKMC	muscle:	n/a
3	chr1:247282458-247282508	HRPEpiC	eye:	n/a
4	chr1:247282458-247282508	HEEpiC	esophagus:	n/a
5	chr1:247282458-247282508	GM06990	blood:	n/a
6	chr1:247282458-247282508	Jurkat	blood:	n/a
7	chr1:247282458-247282508	HCT-116	colon:	n/a
8	chr1:247282458-247282508	AG04449	skin:	fetal
9	chr1:247282458-247282508	PANC-1	pancreas:	n/a
10	chr1:247282458-247282508	HCPEpiC	choroid plexus:	n/a
11	chr1:247282458-247282508	SK-N-MC	brain:	n/a
12	chr1:247282458-247282508	ProgFib	skin:	n/a
13	chr1:247282458-247282508	HUVEC	blood vessel:	n/a
14	chr1:247282458-247282508	SAEC	small airway:	n/a
15	chr1:247282458-247282508	HepG2	liver:	n/a
16	chr1:247282458-247282508	HAEpiC	amniotic membrane:	n/a
17	chr1:247282458-247282508	HRE	kidney:	n/a
18	chr1:247282458-247282508	Hepatocyte	liver:	n/a
19	chr1:247282458-247282508	MCF10A-Er-Src	breast:	n/a
20	chr1:247282458-247282508	BJ	skin:	n/a
21	chr1:247282458-247282508	HL-60	blood:	n/a
22	chr1:247282458-247282508	HMEC	breast:	n/a
23	chr1:247282458-247282508	NB4	blood:	n/a
24	chr1:247282458-247282508	GM12891	blood:	n/a
25	chr1:247282458-247282508	AoSMC	blood vessel:	n/a
26	chr1:247282458-247282508	NH-A	brain:	n/a
27	chr1:247282458-247282508	GM12892	blood:	n/a
28	chr1:247282458-247282508	HPAEpiC	pulmonary alveolar:	n/a
29	chr1:247282458-247282508	HIPEpiC	eye:	n/a
30	chr1:247282458-247282508	Caco-2	colon:	n/a
31	chr1:247282458-247282508	SK-N-SH_RA	brain:	n/a
32	chr1:247282458-247282508	NHDF-neo	bronchial:	n/a
33	chr1:247282458-247282508	AG10803	skin:	n/a
34	chr1:247282458-247282508	Hela-S3	cervix:	n/a
35	chr1:247282458-247282508	K562	blood:	n/a
36	chr1:247282458-247282508	HCF	heart:	n/a
37	chr1:247282458-247282508	RPTEC	kidney:	n/a
38	chr1:247282458-247282508	GM19239	blood:	n/a
39	chr1:247282458-247282508	MCF-7	breast:	n/a
40	chr1:247282458-247282508	T-47D	breast:	n/a
41	chr1:247282458-247282508	HRCEpiC	kidney:	n/a
42	chr1:247282458-247282508	GM12878	blood:	n/a
43	chr1:247282458-247282508	H1-hESC	embryonic stem cell:	embryo
44	chr1:247282458-247282508	HEK293	kidney:	embryo
45	chr1:247282458-247282508	PFSK-1	brain:	n/a
46	chr1:247282458-247282508	PrEC	prostate:	n/a
47	chr1:247282458-247282508	AG09319	gingival:	n/a
48	chr1:247282458-247282508	ovcar-3	ovarian:	n/a
49	chr1:247282458-247282508	LNCaP	prostate:	n/a
50	chr1:247282458-247282508	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr1:247241666..247243646-chr1:247278123..247279948,2	K562	blood:
2	chr1:247274786..247276587-chr1:247277453..247279795,2	MCF-7	breast:
3	chr1:247273239..247275061-chr1:247277041..247280302,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-9	chr1:247282971-247283580	NONHSAT010752

Variant related genes	Relation type
C1orf229	TF binding region
FGFR3P6	TF binding region
C1orf229	CpG island
FGFR3P6	CpG island
ENSG00000221953	chromatin interactions
ENSG00000135747	chromatin interactions

Extended variants
information (count: 115 )
Associated
traits (count: 30 )

Variant overlapped rSNPs/rCNVs (count:115 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs28489280	chr1:247279582-247279583	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs28606523	chr1:247279584-247279585	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs28612339	chr1:247279645-247279646	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs28705205	chr1:247279665-247279666	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs28507145	chr1:247279667-247279668	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs200139656	chr1:247279691-247279692	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs55815441	chr1:247279802-247279803	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs201706516	chr1:247279873-247279874	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs201274933	chr1:247279962-247279963	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs200698161	chr1:247280136-247280137	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs373975432	chr1:247280273-247280274	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs55851721	chr1:247280312-247280313	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs200448724	chr1:247280466-247280467	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs201450624	chr1:247280700-247280701	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs200371324	chr1:247281295-247281296	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs566569058	chr1:247281328-247281329	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs1212570	chr1:247281510-247281511	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs1212898	chr1:247281525-247281526	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs1212899	chr1:247281602-247281603	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs55787515	chr1:247281769-247281770	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs538005065	chr1:247281874-247281875	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs367889905	chr1:247281904-247281905	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs12748377	chr1:247281942-247281943	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs371998562	chr1:247281950-247281951	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs12748386	chr1:247281963-247281964	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs12748393	chr1:247281982-247281983	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs1192845	chr1:247282077-247282078	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs555954667	chr1:247282104-247282105	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs12748601	chr1:247282123-247282124	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs567984731	chr1:247282150-247282151	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs376364523	chr1:247282169-247282170	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs113806528	chr1:247282180-247282181	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs372735385	chr1:247282201-247282202	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs12121338	chr1:247282226-247282227	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs34942837	chr1:247282229-247282230	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs535340511	chr1:247282242-247282243	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs192072164	chr1:247282250-247282251	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs553683571	chr1:247282261-247282262	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs554781698	chr1:247282262-247282263	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs373941114	chr1:247282266-247282267	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs12121363	chr1:247282272-247282273	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs12128943	chr1:247282291-247282292	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs576970648	chr1:247282304-247282305	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs181736145	chr1:247282310-247282311	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs200962231	chr1:247282326-247282327	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs186943660	chr1:247282368-247282369	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs190539161	chr1:247282370-247282371	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs544557610	chr1:247282382-247282383	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs545838259	chr1:247282393-247282394	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs147483032	chr1:247282404-247282405	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:30)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247276600-247284600	Weak transcription	Right Ventricle	heart
2	chr1:247276800-247283000	Weak transcription	Spleen	Spleen
3	chr1:247279000-247290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:247279200-247282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:247282200-247282600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:247282200-247283600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:247282400-247283800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:247282600-247291000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:247283000-247283800	ZNF genes & repeats	Spleen	Spleen

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