Variant report

Variant	nsv873376
Chromosome Location	chr1:242482557-242563708
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	BATF	chr1:242512997-242513219	GM12878	blood:	n/a	n/a
2	BHLHE40	chr1:242555256-242555349	A549	lung:	n/a	n/a
3	CEBPB	chr1:242559279-242559448	HepG2	liver:	n/a	chr1:242559383-242559394 chr1:242559300-242559311
4	CEBPB	chr1:242559268-242559449	A549	lung:	n/a	chr1:242559383-242559394 chr1:242559300-242559311
5	CHD2	chr1:242532487-242532558	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:242513258-242513301	Fibrobl	skin:	n/a	n/a
7	CTCF	chr1:242506679-242506710	GM12878	blood:	n/a	n/a
8	CTCF	chr1:242497815-242497853	A549	lung:	n/a	n/a
9	CTCF	chr1:242500289-242500350	Kidney_OC	kidney:	n/a	n/a
10	CTCF	chr1:242519286-242519337	GM10248	blood:	n/a	n/a
11	CTCF	chr1:242506653-242506767	MCF-7	breast:	n/a	n/a
12	CTCF	chr1:242515346-242515355	Spleen_OC	spleen:	n/a	n/a
13	CTCF	chr1:242506674-242506768	A549	lung:	n/a	n/a
14	CTCF	chr1:242506613-242506789	MCF-7	breast:	n/a	n/a
15	CTCF	chr1:242509007-242509038	GM10266	blood:	n/a	n/a
16	CTCF	chr1:242506744-242506815	GM10248	blood:	n/a	n/a
17	CTCF	chr1:242540509-242540562	GM10266	blood:	n/a	n/a
18	CTCF	chr1:242558022-242558058	Medullo	brain:	n/a	n/a
19	CTCF	chr1:242506631-242506749	K562	blood:	n/a	n/a
20	CTCF	chr1:242544707-242544746	GM20000	blood:	n/a	n/a
21	CTCF	chr1:242500435-242500495	GM13977	blood:	n/a	n/a
22	CTCF	chr1:242495489-242495580	Lung_OC	lung:	n/a	n/a
23	CTCF	chr1:242482738-242482821	GM13976	blood:	n/a	n/a
24	CTCF	chr1:242506653-242506751	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:242497781-242497874	MCF-7	breast:	n/a	n/a
26	CTCF	chr1:242549719-242549814	Fibrobl	skin:	n/a	n/a
27	CTCF	chr1:242521576-242521640	Kidney_OC	kidney:	n/a	n/a
28	CTCF	chr1:242526509-242526586	LNCaP	prostate:	n/a	n/a
29	CTCF	chr1:242506628-242506800	Gliobla	brain:	n/a	n/a
30	CTCF	chr1:242515278-242515333	Spleen_OC	spleen:	n/a	n/a
31	CTCF	chr1:242506671-242506741	GM12892	blood:	n/a	n/a
32	CTCF	chr1:242506620-242506784	HepG2	liver:	n/a	n/a
33	CTCF	chr1:242506662-242506757	ProgFib	skin:	n/a	n/a
34	CTCF	chr1:242483800-242483916	GM20000	blood:	n/a	n/a
35	CTCF	chr1:242508883-242508962	GM20000	blood:	n/a	n/a
36	CTCF	chr1:242523490-242523535	GM13976	blood:	n/a	n/a
37	CTCF	chr1:242530798-242530855	GM20000	blood:	n/a	n/a
38	CTCF	chr1:242506669-242506769	MCF-7	breast:	n/a	n/a
39	E2F4	chr1:242524205-242524400	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr1:242531568-242531652	MCF10A-Er-Src	breast:	n/a	n/a
41	ELK1	chr1:242545423-242545520	Hela-S3	cervix:	n/a	n/a
42	ESR1	chr1:242553690-242553947	T-47D	breast:	n/a	chr1:242553840-242553857 chr1:242553839-242553856
43	FOS	chr1:242494311-242494541	MCF10A-Er-Src	breast:	n/a	chr1:242494407-242494417
44	FOS	chr1:242485413-242485635	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr1:242485426-242485626	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr1:242509617-242509803	MCF10A-Er-Src	breast:	n/a	chr1:242509783-242509790 chr1:242509781-242509790 chr1:242509782-242509790
47	FOS	chr1:242494474-242494495	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr1:242485478-242485633	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr1:242509680-242509850	MCF10A-Er-Src	breast:	n/a	chr1:242509783-242509790 chr1:242509781-242509790 chr1:242509782-242509790
50	FOS	chr1:242509720-242509803	MCF10A-Er-Src	breast:	n/a	chr1:242509783-242509790 chr1:242509781-242509790 chr1:242509782-242509790

No.	Distal block	Cell Line	Cell type
1	chr1:242536607..242538996-chr1:242545702..242547462,2	MCF-7	breast:
2	chr1:242532755..242535089-chr1:242538620..242540939,2	MCF-7	breast:
3	chr1:242536607..242538996-chr1:242545702..242547462,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235467	TF binding region
ENSG00000213690	TF binding region
ENSG00000226750	TF binding region
ENSG00000213690	chromatin interactions

Extended variants
information (count: 3741 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:3741 , 50 per page) page: 1 2 3 4 5 6 7 ... 75

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6674479	chr1:242482557-242482558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs199497538	chr1:242482566-242482567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs187174113	chr1:242482644-242482645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs2796089	chr1:242482658-242482659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs544051574	chr1:242482662-242482663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190105657	chr1:242482673-242482674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs574535158	chr1:242482716-242482717	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs540753677	chr1:242482726-242482727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs182776542	chr1:242482810-242482811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs188427986	chr1:242482824-242482825	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs201765190	chr1:242482852-242482853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs552619264	chr1:242482895-242482896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs562831589	chr1:242482897-242482898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs2937878	chr1:242482944-242482945	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs2937877	chr1:242482952-242482953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs532048446	chr1:242482961-242482962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs193236296	chr1:242482973-242482974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs145254455	chr1:242482974-242482975	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs534117558	chr1:242482994-242482995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs185659700	chr1:242483009-242483010	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs566468536	chr1:242483013-242483014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538304141	chr1:242483028-242483029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs199930116	chr1:242483034-242483035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs187849614	chr1:242483035-242483036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs370856211	chr1:242483078-242483079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs537786227	chr1:242483112-242483113	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554551284	chr1:242483124-242483125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs10926677	chr1:242483127-242483128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs371877709	chr1:242483137-242483138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs574601518	chr1:242483143-242483144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs61847228	chr1:242483149-242483150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs139634456	chr1:242483197-242483198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs540075566	chr1:242483221-242483222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs536282560	chr1:242483241-242483242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs201069744	chr1:242483245-242483246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs202011418	chr1:242483248-242483249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs553896522	chr1:242483251-242483252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200000644	chr1:242483252-242483253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs577424938	chr1:242483255-242483256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs552366192	chr1:242483259-242483260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs12143712	chr1:242483302-242483303	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs191583228	chr1:242483306-242483307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs56763144	chr1:242483329-242483330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs562224680	chr1:242483340-242483341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs113983673	chr1:242483384-242483385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs10926678	chr1:242483405-242483406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs527961454	chr1:242483413-242483414	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs79843480	chr1:242483416-242483417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs77621472	chr1:242483418-242483419	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs79763846	chr1:242483420-242483421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	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
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	21829676	CNVD
Hepatocellular carcinoma	16750200	CNVD
Arrhythmogenic right ventricular cardiomyopathy	17576883	CNVD
Multiple myeloma	16616336	CNVD
Developmental delay	21147756	CNVD
Ovarian cancer	21720365	CNVD
Glioblastoma multiforme	22291905	CNVD
Myelofibrosis	22110671	CNVD
Disease	21936942	CNVD
laryngomalacia	21936942	CNVD
GLUT3 deficiency syndrome	20509907	CNVD
Developmental delay	21373258	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Developmental delay	19490664	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242472600-242485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:242477800-242485400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:242481800-242483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:242481800-242485000	Weak transcription	HMEC	breast
5	chr1:242481800-242485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:242481800-242485400	Weak transcription	Aorta	Aorta
7	chr1:242485000-242486000	Enhancers	HMEC	breast
8	chr1:242485400-242485600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:242485400-242485600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:242485400-242485600	ZNF genes & repeats	Aorta	Aorta
11	chr1:242485400-242486000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:242485600-242485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:242485600-242494400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:242485600-242555400	Weak transcription	Aorta	Aorta
15	chr1:242486000-242488000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:242486800-242487200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:242488000-242488200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:242488000-242488400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:242488200-242508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:242488400-242496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:242491000-242491400	Enhancers	A549	lung
22	chr1:242493400-242493800	Enhancers	Brain Anterior Caudate	brain
23	chr1:242493400-242494600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:242493400-242494800	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:242493600-242494200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:242493600-242494400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:242493600-242494400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:242493600-242494400	Enhancers	Brain Hippocampus Middle	brain
29	chr1:242493600-242494600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:242494200-242494600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:242494200-242494600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:242494400-242494600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:242494400-242494600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:242494400-242494800	Enhancers	Brain Substantia Nigra	brain
35	chr1:242494600-242496200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:242494600-242496600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:242494600-242512400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:242496000-242496600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:242496200-242496600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:242496600-242497600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:242496600-242505200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:242497600-242498000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:242498000-242498400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:242501800-242512000	Weak transcription	HMEC	breast
45	chr1:242502600-242503200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:242502600-242503200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:242503200-242512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:242505200-242506000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:242506000-242512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:242508200-242509000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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