Variant report

Variant	esv2422136
Chromosome Location	chr3:100669517-100673226
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	CTCF	chr3:100672100-100672250	HPAF	blood vessel:	n/a	chr3:100672148-100672157
2	CTCF	chr3:100672100-100672250	HCPEpiC	choroid plexus:	n/a	chr3:100672148-100672157
3	CTCF	chr3:100672100-100672250	AG04450	lung:	n/a	chr3:100672148-100672157
4	CTCF	chr3:100672040-100672190	HCT-116	colon:	n/a	chr3:100672148-100672157
5	CTCF	chr3:100672080-100672230	HVMF	connective:	n/a	chr3:100672148-100672157
6	CTCF	chr3:100672120-100672270	HCT-116	colon:	n/a	chr3:100672148-100672157
7	CTCF	chr3:100672100-100672250	RPTEC	kidney:	n/a	chr3:100672148-100672157
8	CTCF	chr3:100672060-100672210	Hela-S3	cervix:	n/a	chr3:100672148-100672157
9	CTCF	chr3:100672080-100672230	SK-N-SH_RA	brain:	n/a	chr3:100672148-100672157
10	CTCF	chr3:100672060-100672210	HMF	breast:	n/a	chr3:100672148-100672157
11	CTCF	chr3:100672060-100672210	AG04450	lung:	n/a	chr3:100672148-100672157
12	CTCF	chr3:100672060-100672210	HCFaa	heart:	n/a	chr3:100672148-100672157
13	CTCF	chr3:100672160-100672310	HCM	heart:	n/a	n/a
14	CTCF	chr3:100672120-100672270	BE2_C	brain:	n/a	chr3:100672148-100672157
15	CTCF	chr3:100672000-100672150	K562	blood:	n/a	n/a
16	CTCF	chr3:100672080-100672230	HRPEpiC	eye:	n/a	chr3:100672148-100672157
17	CTCF	chr3:100672138-100672249	HUVEC	blood vessel:	n/a	chr3:100672148-100672157
18	CTCF	chr3:100672000-100672150	HRE	kidney:	n/a	n/a
19	CTCF	chr3:100672109-100672221	Hela-S3	cervix:	n/a	chr3:100672148-100672157
20	CTCF	chr3:100672740-100672890	HMF	breast:	n/a	n/a
21	CTCF	chr3:100672000-100672150	HEK293	kidney:	n/a	n/a
22	CTCF	chr3:100671980-100672130	BE2_C	brain:	n/a	n/a
23	CTCF	chr3:100671980-100672130	A549	lung:	n/a	n/a
24	CTCF	chr3:100672000-100672150	HPF	lung:	n/a	n/a
25	CTCF	chr3:100672000-100672150	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:100671980-100672130	HAc	cerebellar:	n/a	n/a
27	CTCF	chr3:100672020-100672170	HBMEC	blood vessel:	n/a	chr3:100672148-100672157
28	CTCF	chr3:100672060-100672210	HBMEC	blood vessel:	n/a	chr3:100672148-100672157
29	CTCF	chr3:100672060-100672210	NHLF	lung:	n/a	chr3:100672148-100672157
30	CTCF	chr3:100672160-100672310	BJ	skin:	n/a	n/a
31	CTCF	chr3:100672160-100672310	NHDF-neo	bronchial:	n/a	n/a
32	CTCF	chr3:100672080-100672230	AoAF	blood vessel:	n/a	chr3:100672148-100672157
33	CTCF	chr3:100672220-100672370	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr3:100672020-100672170	HMF	breast:	n/a	chr3:100672148-100672157
35	CTCF	chr3:100672100-100672250	HRPEpiC	eye:	n/a	chr3:100672148-100672157
36	GATA3	chr3:100673159-100674415	SK-N-SH	brain:	n/a	chr3:100673362-100673372
37	GATA3	chr3:100673206-100674287	SK-N-SH	brain:	n/a	chr3:100673362-100673372
38	MAZ	chr3:100671267-100671382	HepG2	liver:	n/a	n/a
39	NFYA	chr3:100671605-100671756	GM12878	blood:	n/a	n/a
40	TCF12	chr3:100673113-100674390	SK-N-SH	brain:	n/a	n/a
41	USF1	chr3:100672041-100672306	SK-N-SH_RA	brain:	n/a	chr3:100672160-100672181 chr3:100672167-100672176 chr3:100672166-100672175 chr3:100672166-100672175
42	USF1	chr3:100671977-100672304	K562	blood:	n/a	chr3:100672160-100672181 chr3:100672167-100672176 chr3:100672166-100672175 chr3:100672166-100672175
43	USF1	chr3:100671881-100672429	HCT-116	colon:	n/a	chr3:100672160-100672181 chr3:100672167-100672176 chr3:100672166-100672175 chr3:100672166-100672175
44	USF1	chr3:100672061-100672336	SK-N-SH_RA	brain:	n/a	chr3:100672160-100672181 chr3:100672167-100672176 chr3:100672166-100672175 chr3:100672166-100672175

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100667011..100669832-chr3:100673806..100676127,2	K562	blood:

Variant related genes	Relation type
RNU6-865P	TF binding region

Extended variants
information (count: 134 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:134 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556475532	chr3:100669559-100669560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs145603007	chr3:100669563-100669564	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs538827734	chr3:100669569-100669570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs62273935	chr3:100669576-100669577	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs138198857	chr3:100669587-100669588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs543022174	chr3:100669682-100669683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs375207162	chr3:100669697-100669698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs142791899	chr3:100669747-100669748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs144270767	chr3:100669751-100669752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs386663902	chr3:100669851-100669852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs565225768	chr3:100669874-100669875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs532611882	chr3:100669878-100669879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs148747397	chr3:100669925-100669926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs560204661	chr3:100669926-100669927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs141498460	chr3:100669931-100669932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs35760330	chr3:100669956-100669957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs188256093	chr3:100670039-100670040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2164630	chr3:100670061-100670062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs548987712	chr3:100670127-100670128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs567300553	chr3:100670133-100670134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs531318648	chr3:100670147-100670148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs550140694	chr3:100670168-100670169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535964739	chr3:100670226-100670227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs191854158	chr3:100670254-100670255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs553650507	chr3:100670280-100670281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs534516779	chr3:100670281-100670282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs2713752	chr3:100670336-100670337	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs183574394	chr3:100670353-100670354	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs554625536	chr3:100670362-100670363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs547915969	chr3:100670401-100670402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576065280	chr3:100670409-100670410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs543407561	chr3:100670425-100670426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs569299687	chr3:100670444-100670445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs188261006	chr3:100670446-100670447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs7647640	chr3:100670462-100670463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs541629525	chr3:100670489-100670490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs567671522	chr3:100670506-100670507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs559667003	chr3:100670524-100670525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185537754	chr3:100670527-100670528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs2713750	chr3:100670539-100670540	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs560956720	chr3:100670540-100670541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs531382324	chr3:100670577-100670578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs549751629	chr3:100670610-100670611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs7613669	chr3:100670633-100670634	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs532276872	chr3:100670639-100670640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs369438406	chr3:100670654-100670655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs145653190	chr3:100670676-100670677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs536435422	chr3:100670702-100670703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs76458280	chr3:100670705-100670706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs190413851	chr3:100670750-100670751	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Breast cancer	16608533	CNVD
Breast cancer	21785460	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100630200-100673600	Weak transcription	Ovary	ovary
2	chr3:100660600-100673200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:100660600-100673600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:100660600-100673600	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:100660800-100672800	Weak transcription	HSMM	muscle
6	chr3:100667000-100675600	Weak transcription	Aorta	Aorta
7	chr3:100667400-100671600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:100667400-100672200	Weak transcription	NHDF-Ad	bronchial
9	chr3:100667400-100672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:100667400-100672600	Weak transcription	Osteobl	bone
11	chr3:100667400-100673400	Weak transcription	Fetal Stomach	stomach
12	chr3:100668600-100671800	Weak transcription	HSMMtube	muscle
13	chr3:100669400-100672400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:100671600-100673200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:100671800-100674000	Enhancers	HSMMtube	muscle
16	chr3:100671800-100677200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:100672000-100672200	Enhancers	Colon Smooth Muscle	Colon
18	chr3:100672200-100673600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:100672200-100675200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:100672200-100677200	Enhancers	NHDF-Ad	bronchial
21	chr3:100672400-100673200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:100672600-100673200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:100672600-100677200	Enhancers	Osteobl	bone
24	chr3:100672800-100674000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:100672800-100674200	Enhancers	HSMM	muscle
26	chr3:100672800-100674200	Enhancers	HUVEC	blood vessel
27	chr3:100672800-100674600	Enhancers	NHEK	skin
28	chr3:100673200-100673600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:100673200-100673800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:100673200-100673800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100673200-100674000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:100673200-100674000	Enhancers	NHLF	lung
33	chr3:100673200-100674200	Enhancers	Fetal Lung	lung
34	chr3:100673200-100674400	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:100673200-100674400	Enhancers	HMEC	breast
36	chr3:100673200-100674600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:100673200-100675400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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