Variant report

Variant	esv3425103
Chromosome Location	chr2:54305541-54309163
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	ATF1	chr2:54308755-54309212	K562	blood:	n/a	n/a
2	ATF2	chr2:54308540-54309302	GM12878	blood:	n/a	n/a
3	ATF2	chr2:54308473-54309250	GM12878	blood:	n/a	n/a
4	ATF3	chr2:54308720-54309207	K562	blood:	n/a	n/a
5	ATF3	chr2:54308822-54309096	K562	blood:	n/a	n/a
6	BATF	chr2:54308614-54309143	GM12878	blood:	n/a	chr2:54308907-54308918 chr2:54308908-54308918 chr2:54308912-54308922
7	BATF	chr2:54308598-54309166	GM12878	blood:	n/a	chr2:54308907-54308918 chr2:54308908-54308918 chr2:54308912-54308922
8	BCL11A	chr2:54308579-54309128	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
9	BCL11A	chr2:54308658-54309115	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
10	BCL3	chr2:54308620-54309160	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
11	BCLAF1	chr2:54308645-54309174	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
12	BCLAF1	chr2:54308385-54309255	GM12878	blood:	n/a	chr2:54308929-54308938 chr2:54309019-54309026
13	BHLHE40	chr2:54308767-54309165	K562	blood:	n/a	n/a
14	BHLHE40	chr2:54308623-54309223	GM12878	blood:	n/a	chr2:54309198-54309214
15	CBX3	chr2:54304383-54305691	K562	blood:	n/a	n/a
16	CBX3	chr2:54308334-54309249	K562	blood:	n/a	n/a
17	CEBPB	chr2:54308509-54309337	GM12878	blood:	n/a	chr2:54309304-54309317
18	CEBPB	chr2:54308790-54309156	K562	blood:	n/a	n/a
19	CEBPB	chr2:54308671-54309130	GM12878	blood:	n/a	n/a
20	CEBPB	chr2:54308670-54309219	K562	blood:	n/a	n/a
21	CEBPB	chr2:54308568-54308967	ECC-1	luminal epithelium:	n/a	n/a
22	CEBPB	chr2:54305604-54305700	K562	blood:	n/a	chr2:54305637-54305650
23	CEBPD	chr2:54308708-54309272	K562	blood:	n/a	n/a
24	CEBPD	chr2:54308778-54309296	K562	blood:	n/a	n/a
25	CHD2	chr2:54308648-54309147	GM12878	blood:	n/a	n/a
26	CREB1	chr2:54308498-54309282	GM12878	blood:	n/a	n/a
27	CREB1	chr2:54308427-54309326	GM12878	blood:	n/a	n/a
28	CTCF	chr2:54308820-54308970	SAEC	small airway:	n/a	n/a
29	CTCF	chr2:54308919-54309003	GM19238	blood:	n/a	n/a
30	CTCF	chr2:54308889-54309035	GM19239	blood:	n/a	n/a
31	CTCF	chr2:54308916-54308944	GM13976	blood:	n/a	n/a
32	CTCF	chr2:54308900-54309050	HCPEpiC	choroid plexus:	n/a	n/a
33	CTCF	chr2:54308933-54308996	GM19240	blood:	n/a	n/a
34	CTCF	chr2:54308919-54309019	GM12892	blood:	n/a	n/a
35	CTCF	chr2:54308860-54309010	HMEC	breast:	n/a	n/a
36	CTCF	chr2:54308860-54309010	GM12870	blood:	n/a	n/a
37	CTCF	chr2:54308900-54309050	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr2:54308958-54308976	NHEK	skin:	n/a	n/a
39	CTCF	chr2:54308796-54309115	GM12878	blood:	n/a	n/a
40	CTCF	chr2:54308820-54308970	HEEpiC	esophagus:	n/a	n/a
41	CTCF	chr2:54308862-54309062	K562	blood:	n/a	n/a
42	CTCF	chr2:54308893-54309016	GM12891	blood:	n/a	n/a
43	CTCF	chr2:54308860-54309010	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr2:54308720-54308870	GM12872	blood:	n/a	n/a
45	CTCF	chr2:54308919-54308975	GM13977	blood:	n/a	n/a
46	CUX1	chr2:54308677-54309181	GM12878	blood:	n/a	n/a
47	EBF1	chr2:54308782-54309036	GM12878	blood:	n/a	n/a
48	EBF1	chr2:54308636-54309097	GM12878	blood:	n/a	n/a
49	EBF1	chr2:54308597-54309145	GM12878	blood:	n/a	n/a
50	EGR1	chr2:54308765-54309038	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:190092651..190093439-chr2:54308392..54308957,2	MCF-7	breast:
2	chr2:54304842..54306570-chr2:54310702..54313482,3	K562	blood:
3	chr2:54299748..54301680-chr2:54304103..54306352,2	K562	blood:
4	chr2:54303600..54306437-chr2:54307043..54310223,4	K562	blood:
5	chr2:54303310..54306490-chr2:54307537..54312281,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSME4-2	chr2:54307069-54307599	NONHSAT070719
2	lnc-PSME4-2	chr2:54307111-54307417	NONHSAT070726
3	lnc-ACYP2-1	chr2:54307069-54307601	ENSG00000239235.3

Variant related genes	Relation type
ENSG00000241114	TF binding region
ENSG00000272156	TF binding region
ENSG00000241114	chromatin interactions
ENSG00000272156	chromatin interactions

Extended variants
information (count: 143 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:143 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs199712886	chr2:54305548-54305549	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs376716931	chr2:54305549-54305550	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs56411409	chr2:54305554-54305555	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs201068950	chr2:54305561-54305562	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs397738329	chr2:54305573-54305574	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs566133352	chr2:54305589-54305590	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs534493969	chr2:54305617-54305618	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs528656542	chr2:54305638-54305639	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs548921206	chr2:54305639-54305640	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs568736178	chr2:54305690-54305691	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs11326614	chr2:54305742-54305743	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs7600141	chr2:54305797-54305798	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs557049779	chr2:54305798-54305799	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs7573551	chr2:54305801-54305802	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs539540594	chr2:54305820-54305821	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs141806060	chr2:54305854-54305855	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs150593408	chr2:54305897-54305898	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs183865467	chr2:54305946-54305947	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs577400120	chr2:54305992-54305993	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs554461845	chr2:54306030-54306031	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs370643440	chr2:54306032-54306033	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs543044209	chr2:54306054-54306055	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs117907166	chr2:54306055-54306056	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs959286	chr2:54306078-54306079	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs959285	chr2:54306101-54306102	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs559353769	chr2:54306108-54306109	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs546500354	chr2:54306172-54306173	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs139554877	chr2:54306219-54306220	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs548784766	chr2:54306235-54306236	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs568797243	chr2:54306302-54306303	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs531226848	chr2:54306305-54306306	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs369503226	chr2:54306328-54306329	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs550991551	chr2:54306332-54306333	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs570764641	chr2:54306336-54306337	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs539771826	chr2:54306371-54306372	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs374640815	chr2:54306381-54306382	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs149719794	chr2:54306421-54306422	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs541688287	chr2:54306447-54306448	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs10496028	chr2:54306454-54306455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs147472411	chr2:54306457-54306458	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs372025726	chr2:54306475-54306476	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs140020978	chr2:54306495-54306496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs114942561	chr2:54306501-54306502	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs553547811	chr2:54306565-54306566	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs188757073	chr2:54306567-54306568	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs576767049	chr2:54306606-54306607	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs545756932	chr2:54306655-54306656	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs559216070	chr2:54306702-54306703	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs572952085	chr2:54306743-54306744	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs542487267	chr2:54306746-54306747	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54310000	Weak transcription	Ovary	ovary
2	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
5	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:54292000-54308400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:54293000-54306000	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:54293200-54306200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54293200-54306200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:54293400-54308400	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:54293600-54310600	Weak transcription	HSMM	muscle
16	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:54295400-54309800	Weak transcription	Fetal Brain Male	brain
19	chr2:54301600-54308200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:54302200-54308200	Weak transcription	HMEC	breast
21	chr2:54302200-54310600	Weak transcription	A549	lung
22	chr2:54302600-54308600	Weak transcription	NH-A	brain
23	chr2:54302600-54310400	Weak transcription	Osteobl	bone
24	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
25	chr2:54305000-54306200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:54305000-54308000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:54305000-54315000	Weak transcription	Fetal Intestine Large	intestine
28	chr2:54305000-54315200	Weak transcription	Pancreas	Pancrea
29	chr2:54305400-54306200	Enhancers	K562	blood
30	chr2:54305400-54321600	Weak transcription	Lung	lung
31	chr2:54306000-54306400	Enhancers	Brain Substantia Nigra	brain
32	chr2:54306000-54306600	Enhancers	Brain Hippocampus Middle	brain
33	chr2:54306200-54306400	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:54306200-54307400	Enhancers	Brain Anterior Caudate	brain
35	chr2:54306200-54307400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:54306200-54307400	ZNF genes & repeats	K562	blood
37	chr2:54306400-54306600	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr2:54306400-54306800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:54306400-54306800	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr2:54306400-54307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:54306400-54307800	Enhancers	Brain Angular Gyrus	brain
42	chr2:54306600-54306800	Active TSS	Brain Cingulate Gyrus	brain
43	chr2:54306600-54307400	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:54306600-54315400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:54306800-54307400	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:54306800-54307600	Enhancers	Brain Substantia Nigra	brain
47	chr2:54307000-54307400	Strong transcription	Primary T cells from cord blood	blood
48	chr2:54307400-54308200	Enhancers	Brain Hippocampus Middle	brain
49	chr2:54307400-54308400	Weak transcription	K562	blood
50	chr2:54307400-54309800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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