Variant report

Variant	nsv529013
Chromosome Location	chr3:142877227-142888043
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	ARID3A	chr3:142887160-142887701	K562	blood:	n/a	n/a
2	ARID3A	chr3:142884555-142884662	K562	blood:	n/a	n/a
3	ATF1	chr3:142884502-142884840	K562	blood:	n/a	n/a
4	ATF1	chr3:142887275-142887709	K562	blood:	n/a	n/a
5	ATF2	chr3:142877219-142877968	GM12878	blood:	n/a	n/a
6	ATF2	chr3:142883498-142884818	GM12878	blood:	n/a	n/a
7	ATF2	chr3:142876783-142877936	GM12878	blood:	n/a	n/a
8	ATF2	chr3:142883476-142884102	GM12878	blood:	n/a	n/a
9	ATF2	chr3:142884217-142884797	GM12878	blood:	n/a	n/a
10	ATF3	chr3:142884466-142884763	K562	blood:	n/a	n/a
11	ATF3	chr3:142887373-142887703	K562	blood:	n/a	n/a
12	BATF	chr3:142884528-142884761	GM12878	blood:	n/a	n/a
13	BATF	chr3:142876880-142877317	GM12878	blood:	n/a	n/a
14	BATF	chr3:142883729-142884024	GM12878	blood:	n/a	n/a
15	BATF	chr3:142883652-142884050	GM12878	blood:	n/a	n/a
16	BATF	chr3:142877358-142877838	GM12878	blood:	n/a	n/a
17	BATF	chr3:142876551-142877851	GM12878	blood:	n/a	n/a
18	BATF	chr3:142884468-142884777	GM12878	blood:	n/a	n/a
19	BCL11A	chr3:142876924-142877894	GM12878	blood:	n/a	chr3:142877585-142877594 chr3:142877584-142877593
20	BCL11A	chr3:142883668-142884076	GM12878	blood:	n/a	n/a
21	BCL11A	chr3:142876952-142877287	GM12878	blood:	n/a	n/a
22	BCL11A	chr3:142884480-142884778	GM12878	blood:	n/a	chr3:142884671-142884680 chr3:142884670-142884679
23	BCL11A	chr3:142884551-142884779	GM12878	blood:	n/a	chr3:142884671-142884680 chr3:142884670-142884679
24	BCL11A	chr3:142877500-142877784	GM12878	blood:	n/a	chr3:142877585-142877594 chr3:142877584-142877593
25	BCL3	chr3:142877402-142877822	GM12878	blood:	n/a	chr3:142877585-142877594 chr3:142877584-142877593
26	BCL3	chr3:142883521-142884049	GM12878	blood:	n/a	n/a
27	BCLAF1	chr3:142877259-142878000	GM12878	blood:	n/a	chr3:142877585-142877594 chr3:142877584-142877593
28	BCLAF1	chr3:142883450-142884081	GM12878	blood:	n/a	n/a
29	BCLAF1	chr3:142884384-142884804	GM12878	blood:	n/a	chr3:142884671-142884680 chr3:142884670-142884679
30	BCLAF1	chr3:142876844-142877276	GM12878	blood:	n/a	n/a
31	BHLHE40	chr3:142884533-142884849	K562	blood:	n/a	n/a
32	BHLHE40	chr3:142876609-142877875	GM12878	blood:	n/a	n/a
33	BHLHE40	chr3:142887394-142887703	K562	blood:	n/a	n/a
34	CBX3	chr3:142887276-142888091	K562	blood:	n/a	n/a
35	CBX3	chr3:142884408-142884804	K562	blood:	n/a	n/a
36	CCNT2	chr3:142884556-142884757	K562	blood:	n/a	n/a
37	CCNT2	chr3:142887290-142887770	K562	blood:	n/a	chr3:142887495-142887515
38	CEBPB	chr3:142886812-142887143	Hela-S3	cervix:	n/a	n/a
39	CEBPB	chr3:142887265-142887639	K562	blood:	n/a	chr3:142887490-142887501
40	CEBPB	chr3:142887455-142887614	K562	blood:	n/a	chr3:142887490-142887501
41	CEBPB	chr3:142876742-142877313	ECC-1	luminal epithelium:	n/a	n/a
42	CEBPB	chr3:142883198-142884304	GM12878	blood:	n/a	n/a
43	CEBPB	chr3:142886768-142887168	IMR90	lung:	n/a	n/a
44	CEBPD	chr3:142887192-142887760	K562	blood:	n/a	n/a
45	CTCF	chr3:142877760-142877910	GM12874	blood:	n/a	n/a
46	CTCF	chr3:142877753-142877823	GM19240	blood:	n/a	n/a
47	CTCF	chr3:142877717-142877818	GM19238	blood:	n/a	n/a
48	CTCF	chr3:142877720-142877870	GM12878	blood:	n/a	n/a
49	CTCF	chr3:142877720-142877870	GM12865	blood:	n/a	n/a
50	CTCF	chr3:142877680-142877830	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142863143..142865684-chr3:142879611..142883085,3	K562	blood:
2	chr3:142878953..142880947-chr3:142881192..142883078,2	K562	blood:
3	chr3:142887670..142889227-chr3:142893884..142896662,2	K562	blood:
4	chr3:142875650..142878540-chr3:142902217..142903747,2	K562	blood:
5	chr3:142775856..142778240-chr3:142884608..142886181,2	K562	blood:
6	chr3:142871516..142874257-chr3:142874409..142878539,5	K562	blood:
7	chr3:142841180..142845810-chr3:142884202..142887242,4	K562	blood:
8	chr3:142878953..142880947-chr3:142881192..142883078,2	K562	blood:
9	chr3:142837036..142839934-chr3:142882781..142884331,2	K562	blood:
10	chr3:142877084..142878640-chr3:142882606..142885424,2	K562	blood:
11	chr3:142882417..142885348-chr3:142887165..142889309,2	K562	blood:
12	chr3:142842351..142844405-chr3:142885462..142887277,2	K562	blood:
13	chr3:142842296..142843845-chr3:142877160..142879229,2	K562	blood:

Variant related genes	Relation type
ENSG00000211483	TF binding region
ENSG00000241679	chromatin interactions
ENSG00000244171	chromatin interactions
ENSG00000211483	chromatin interactions
ENSG00000175040	chromatin interactions

Extended variants
information (count: 430 )
Associated
traits (count: 50 )

Variant overlapped rSNPs/rCNVs (count:430 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10804687	chr3:142877227-142877228	Enhancers Strong transcription Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs529382499	chr3:142877247-142877248	Enhancers Strong transcription Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs547521634	chr3:142877329-142877330	Enhancers Strong transcription Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs59889913	chr3:142877350-142877351	Enhancers Strong transcription Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs186388890	chr3:142877408-142877409	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs559551262	chr3:142877471-142877472	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs34254150	chr3:142877484-142877485	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs375871509	chr3:142877492-142877493	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs558856931	chr3:142877493-142877494	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs145314713	chr3:142877518-142877519	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs570680180	chr3:142877542-142877543	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs67894485	chr3:142877569-142877570	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs375019287	chr3:142877601-142877602	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs188391102	chr3:142877604-142877605	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs375224643	chr3:142877625-142877626	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs368197366	chr3:142877709-142877710	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs371951806	chr3:142877777-142877778	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs57110037	chr3:142877794-142877795	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs541902772	chr3:142877803-142877804	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs553354028	chr3:142877842-142877843	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs571665269	chr3:142877854-142877855	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs180865318	chr3:142877875-142877876	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs113718799	chr3:142877963-142877964	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs564470765	chr3:142878032-142878033	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs13075966	chr3:142878066-142878067	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs185796955	chr3:142878100-142878101	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs543700892	chr3:142878164-142878165	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs1463215	chr3:142878203-142878204	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs112036122	chr3:142878267-142878268	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs4564940	chr3:142878275-142878276	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs566095630	chr3:142878306-142878307	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs115769946	chr3:142878313-142878314	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs568683408	chr3:142878346-142878347	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs551777555	chr3:142878365-142878366	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs570688941	chr3:142878373-142878374	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs191436577	chr3:142878397-142878398	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs182857202	chr3:142878407-142878408	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs137954159	chr3:142878423-142878424	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs142444860	chr3:142878426-142878427	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs553415413	chr3:142878463-142878464	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs1463216	chr3:142878466-142878467	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs532479671	chr3:142878474-142878475	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs545430887	chr3:142878501-142878502	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs550712315	chr3:142878521-142878522	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs553341431	chr3:142878569-142878570	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs569394212	chr3:142878590-142878591	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs576714313	chr3:142878609-142878610	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs544047907	chr3:142878620-142878621	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs145956201	chr3:142878655-142878656	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs574145139	chr3:142878676-142878677	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:50)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD

Chromatin state (count:272 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142873200-142878800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr3:142873400-142881400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:142873400-142881800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:142876400-142877800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:142876600-142877600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr3:142876600-142878200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:142876600-142878200	Enhancers	HSMM	muscle
8	chr3:142876800-142877400	Strong transcription	Primary T cells from cord blood	blood
9	chr3:142876800-142877400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:142876800-142877800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:142876800-142877800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:142876800-142877800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:142876800-142878000	Enhancers	HMEC	breast
14	chr3:142876800-142878000	Enhancers	NHEK	skin
15	chr3:142876800-142878200	Enhancers	NHDF-Ad	bronchial
16	chr3:142877000-142877400	Flanking Active TSS	GM12878-XiMat	blood
17	chr3:142877000-142877600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:142877000-142877600	Enhancers	Fetal Muscle Leg	muscle
19	chr3:142877000-142877800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:142877000-142877800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:142877000-142877800	Enhancers	Psoas Muscle	Psoas
22	chr3:142877000-142877800	Enhancers	Thymus	Thymus
23	chr3:142877000-142877800	Enhancers	NH-A	brain
24	chr3:142877000-142878000	Enhancers	HSMMtube	muscle
25	chr3:142877000-142878000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:142877000-142878200	Enhancers	Fetal Thymus	thymus
27	chr3:142877000-142879800	Enhancers	Dnd41	blood
28	chr3:142877200-142877600	Enhancers	Hela-S3	cervix
29	chr3:142877200-142877800	Enhancers	Osteobl	bone
30	chr3:142877400-142877800	Enhancers	GM12878-XiMat	blood
31	chr3:142877400-142881200	Weak transcription	Primary T cells from cord blood	blood
32	chr3:142877600-142877800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:142877600-142879000	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:142877800-142878600	Flanking Active TSS	GM12878-XiMat	blood
35	chr3:142877800-142879000	Weak transcription	Psoas Muscle	Psoas
36	chr3:142877800-142879000	Weak transcription	Thymus	Thymus
37	chr3:142877800-142879200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:142877800-142879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:142877800-142884200	Weak transcription	Osteobl	bone
40	chr3:142877800-142886000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:142878000-142881600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:142878200-142879200	Weak transcription	Fetal Thymus	thymus
43	chr3:142878200-142879400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:142878200-142884200	Weak transcription	NHDF-Ad	bronchial
45	chr3:142878600-142879400	Enhancers	GM12878-XiMat	blood
46	chr3:142878800-142880400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:142879000-142879400	Enhancers	Fetal Lung	lung
48	chr3:142879000-142879400	Enhancers	K562	blood
49	chr3:142879000-142879600	Enhancers	Fetal Muscle Leg	muscle
50	chr3:142879200-142879400	Enhancers	Psoas Muscle	Psoas

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