Variant report

Variant	esv3489589
Chromosome Location	chr1:227444279-227450327
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:147)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr1:227444491-227444687	K562	blood:	n/a	n/a
2	ARID3A	chr1:227448086-227448709	K562	blood:	n/a	n/a
3	BHLHE40	chr1:227448130-227448424	K562	blood:	n/a	n/a
4	CBX3	chr1:227448012-227448616	K562	blood:	n/a	n/a
5	CCNT2	chr1:227448099-227448516	K562	blood:	n/a	chr1:227448339-227448359
6	CEBPB	chr1:227448104-227448470	K562	blood:	n/a	n/a
7	CEBPB	chr1:227448026-227448660	K562	blood:	n/a	n/a
8	CEBPD	chr1:227447955-227448536	K562	blood:	n/a	n/a
9	CEBPD	chr1:227447950-227448584	K562	blood:	n/a	n/a
10	CHD1	chr1:227447090-227447093	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr1:227445720-227445725	HepG2	liver:	n/a	n/a
12	CTCF	chr1:227445703-227445931	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:227445721-227445914	Gliobla	brain:	n/a	n/a
14	CTCF	chr1:227448115-227448422	K562	blood:	n/a	n/a
15	CTCF	chr1:227445620-227445770	RPTEC	kidney:	n/a	n/a
16	CTCF	chr1:227445715-227445919	MCF-7	breast:	n/a	n/a
17	CTCF	chr1:227445780-227445930	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:227445700-227445850	HCPEpiC	choroid plexus:	n/a	n/a
19	CTCF	chr1:227445860-227446010	GM12871	blood:	n/a	n/a
20	CTCF	chr1:227445700-227445850	HBMEC	blood vessel:	n/a	n/a
21	CTCF	chr1:227445764-227445872	GM12892	blood:	n/a	n/a
22	CTCF	chr1:227445740-227445890	HPAF	blood vessel:	n/a	n/a
23	CTCF	chr1:227445740-227445890	MCF-7	breast:	n/a	n/a
24	CTCF	chr1:227445760-227445910	K562	blood:	n/a	n/a
25	CTCF	chr1:227445740-227445890	HCFaa	heart:	n/a	n/a
26	CTCF	chr1:227445760-227445910	HEK293	kidney:	n/a	n/a
27	CTCF	chr1:227445665-227445951	K562	blood:	n/a	n/a
28	CTCF	chr1:227445800-227445950	Caco-2	colon:	n/a	n/a
29	CTCF	chr1:227445760-227445910	HMF	breast:	n/a	n/a
30	CTCF	chr1:227445800-227445950	SAEC	small airway:	n/a	n/a
31	CTCF	chr1:227445628-227446012	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr1:227445780-227445930	AG09309	skin:	n/a	n/a
33	CTCF	chr1:227445740-227445890	HA-sp	spinal cord:	n/a	n/a
34	CTCF	chr1:227445643-227445953	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr1:227445740-227445890	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr1:227445731-227445872	Fibrobl	skin:	n/a	n/a
37	CTCF	chr1:227445660-227445810	GM12872	blood:	n/a	n/a
38	CTCF	chr1:227445720-227445916	K562	blood:	n/a	n/a
39	CTCF	chr1:227445820-227445970	HCM	heart:	n/a	n/a
40	CTCF	chr1:227445700-227445850	HCT-116	colon:	n/a	n/a
41	CTCF	chr1:227445680-227445830	A549	lung:	n/a	n/a
42	CTCF	chr1:227445660-227445810	RPTEC	kidney:	n/a	n/a
43	CTCF	chr1:227445680-227445830	GM12869	blood:	n/a	n/a
44	CTCF	chr1:227445800-227445950	GM12874	blood:	n/a	n/a
45	CTCF	chr1:227445760-227445910	HUVEC	blood vessel:	n/a	n/a
46	CTCF	chr1:227445582-227445989	K562	blood:	n/a	n/a
47	CTCF	chr1:227445740-227445890	HCM	heart:	n/a	n/a
48	CTCF	chr1:227445733-227445879	NHEK	skin:	n/a	n/a
49	CTCF	chr1:227445720-227445870	Caco-2	colon:	n/a	n/a
50	CTCF	chr1:227445732-227445920	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:227446023..227447555-chr1:227505720..227507442,2	K562	blood:
2	chr1:227442920..227447581-chr1:227503938..227508329,6	K562	blood:
3	chr1:227442920..227445120-chr1:227505112..227507012,2	K562	blood:
4	chr1:227445055..227447131-chr1:227475888..227477429,2	K562	blood:
5	chr1:227447102..227448619-chr1:227452855..227454756,2	K562	blood:
6	chr1:227446907..227449535-chr1:227450206..227452004,2	K562	blood:
7	chr1:227446907..227449535-chr1:227450206..227452004,2	K562	blood:
8	chr1:227441285..227444497-chr1:227452902..227455834,3	K562	blood:
9	chr1:227447057..227450743-chr1:227504946..227508409,3	MCF-7	breast:

No data

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000236636	chromatin interactions
ENSG00000143776	chromatin interactions

Extended variants
information (count: 251 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:251 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187166595	chr1:227444296-227444297	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs548885295	chr1:227444323-227444324	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs530917579	chr1:227444324-227444325	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs142860748	chr1:227444416-227444417	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs115933907	chr1:227444420-227444421	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs528409083	chr1:227444429-227444430	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs2670466	chr1:227444457-227444458	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs568252621	chr1:227444464-227444465	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs535155926	chr1:227444571-227444572	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs376480662	chr1:227444619-227444620	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs139902680	chr1:227444636-227444637	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs568648726	chr1:227444639-227444640	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs147293340	chr1:227444640-227444641	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs112920956	chr1:227444641-227444642	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs374958848	chr1:227444643-227444644	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs368986167	chr1:227444645-227444646	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs111508327	chr1:227444649-227444650	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs150552441	chr1:227444650-227444651	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs201432745	chr1:227444655-227444656	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs55961981	chr1:227444686-227444687	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs34923911	chr1:227444687-227444688	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs552501278	chr1:227444690-227444691	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs2813962	chr1:227444704-227444705	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs151046228	chr1:227444737-227444738	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs574974762	chr1:227444745-227444746	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs182057205	chr1:227444753-227444754	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs187629678	chr1:227444861-227444862	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs563756084	chr1:227444876-227444877	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs571821547	chr1:227444925-227444926	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs193224854	chr1:227444954-227444955	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs564518045	chr1:227445010-227445011	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs528332021	chr1:227445011-227445012	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs117349515	chr1:227445028-227445029	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs142338985	chr1:227445082-227445083	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs529072276	chr1:227445092-227445093	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs73096374	chr1:227445096-227445097	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs568585748	chr1:227445127-227445128	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs139625594	chr1:227445185-227445186	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs185659850	chr1:227445187-227445188	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs145838525	chr1:227445188-227445189	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs149311050	chr1:227445189-227445190	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs56125060	chr1:227445190-227445191	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs181844210	chr1:227445196-227445197	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs114263100	chr1:227445204-227445205	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs550921027	chr1:227445220-227445221	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs566467294	chr1:227445238-227445239	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs2813963	chr1:227445254-227445255	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs542688093	chr1:227445266-227445267	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs553621617	chr1:227445268-227445269	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs568692927	chr1:227445303-227445304	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	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
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	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
Prostate cancer	18632612	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
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	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
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227425400-227445200	Weak transcription	Osteobl	bone
5	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
6	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
7	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:227432800-227446000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227433000-227446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:227433000-227446000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
14	chr1:227433200-227452800	Weak transcription	Ovary	ovary
15	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
19	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
20	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
21	chr1:227434400-227446000	Weak transcription	Brain Substantia Nigra	brain
22	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:227438800-227448000	Weak transcription	Psoas Muscle	Psoas
27	chr1:227438800-227449400	Weak transcription	Right Atrium	heart
28	chr1:227440000-227456600	Weak transcription	HepG2	liver
29	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
30	chr1:227441200-227450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:227441800-227449600	Weak transcription	A549	lung
32	chr1:227441800-227452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227442400-227449600	Weak transcription	Brain Angular Gyrus	brain
34	chr1:227443200-227446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:227443400-227445400	Weak transcription	K562	blood
36	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:227445200-227445400	Enhancers	Osteobl	bone
38	chr1:227445400-227445600	Enhancers	K562	blood
39	chr1:227445600-227445800	Enhancers	Pancreas	Pancrea
40	chr1:227445600-227446200	Flanking Active TSS	K562	blood
41	chr1:227445800-227448000	Weak transcription	Pancreas	Pancrea
42	chr1:227445800-227458400	Weak transcription	NHEK	skin
43	chr1:227446000-227446200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:227446000-227446400	Enhancers	Brain Substantia Nigra	brain
45	chr1:227446000-227447400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:227446000-227448600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:227446200-227446600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:227446200-227448000	Enhancers	K562	blood
49	chr1:227446400-227446600	Weak transcription	Brain Substantia Nigra	brain
50	chr1:227446600-227447000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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