Variant report

Variant	esv2755718
Chromosome Location	chr3:94887527-94970627
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	BRCA1	chr3:94916763-94916781	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:94908207-94908561	HepG2	liver:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
3	CEBPB	chr3:94908276-94908544	K562	blood:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
4	CEBPB	chr3:94908217-94908539	A549	lung:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
5	CEBPB	chr3:94908204-94908562	IMR90	lung:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
6	CTCF	chr3:94891049-94891134	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr3:94891065-94891193	MCF-7	breast:	n/a	n/a
8	CTCF	chr3:94891040-94891190	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr3:94902980-94903130	K562	blood:	n/a	n/a
10	CTCF	chr3:94902980-94903130	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr3:94902939-94903113	HepG2	liver:	n/a	n/a
12	CTCF	chr3:94903020-94903170	MCF-7	breast:	n/a	n/a
13	CTCF	chr3:94902959-94903153	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:94902920-94903070	WERI-Rb-1	eye:	n/a	n/a
15	CTCF	chr3:94959680-94959830	GM12869	blood:	n/a	n/a
16	CTCF	chr3:94902900-94903050	GM12878	blood:	n/a	n/a
17	CTCF	chr3:94901753-94901799	GM20000	blood:	n/a	n/a
18	CTCF	chr3:94902900-94903050	GM12872	blood:	n/a	n/a
19	CTCF	chr3:94903031-94903125	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:94902943-94903149	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:94902940-94903090	Caco-2	colon:	n/a	n/a
22	CTCF	chr3:94902980-94903130	HepG2	liver:	n/a	n/a
23	CTCF	chr3:94891140-94891290	RPTEC	kidney:	n/a	n/a
24	CTCF	chr3:94902920-94903070	GM12872	blood:	n/a	n/a
25	CTCF	chr3:94944143-94944233	GM13977	blood:	n/a	n/a
26	CTCF	chr3:94959740-94959890	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:94903021-94903076	GM12891	blood:	n/a	n/a
28	CTCF	chr3:94959816-94959863	MCF-7	breast:	n/a	n/a
29	CTCF	chr3:94891080-94891230	RPTEC	kidney:	n/a	n/a
30	CTCF	chr3:94891040-94891190	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr3:94891000-94891150	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:94902980-94903130	HEK293	kidney:	n/a	n/a
33	CTCF	chr3:94903002-94903066	A549	lung:	n/a	n/a
34	CTCF	chr3:94891000-94891150	HRE	kidney:	n/a	n/a
35	CTCF	chr3:94891048-94891194	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:94902980-94903130	GM12875	blood:	n/a	n/a
37	CTCF	chr3:94891020-94891170	HRE	kidney:	n/a	n/a
38	CTCF	chr3:94901413-94901515	Kidney_OC	kidney:	n/a	n/a
39	CTCF	chr3:94902951-94903127	Gliobla	brain:	n/a	n/a
40	CTCF	chr3:94902900-94903050	A549	lung:	n/a	n/a
41	CTCF	chr3:94902960-94903110	HepG2	liver:	n/a	n/a
42	CTCF	chr3:94902994-94903102	GM12892	blood:	n/a	n/a
43	CTCF	chr3:94890940-94891090	BE2_C	brain:	n/a	n/a
44	CTCF	chr3:94900820-94900858	Spleen_OC	spleen:	n/a	n/a
45	CTCF	chr3:94902919-94903180	K562	blood:	n/a	n/a
46	CTCF	chr3:94902937-94903191	GM12878	blood:	n/a	n/a
47	CTCF	chr3:94959660-94959810	HepG2	liver:	n/a	n/a
48	CTCF	chr3:94902951-94903139	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:94902957-94903127	K562	blood:	n/a	n/a
50	CTCF	chr3:94959824-94959858	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62608866..62609588-chr3:94930688..94931197,2	Hela-S3	cervix:
2	chr3:94912857..94914770-chr3:94921596..94924370,2	MCF-7	breast:
3	chr3:94969252..94971265-chr3:94976399..94979300,2	MCF-7	breast:
4	chr3:94934431..94935951-chr3:94936179..94938719,2	K562	blood:
5	chr3:94881976..94883745-chr3:94887711..94889312,2	K562	blood:
6	chr21:43976463..43979311-chr3:94964978..94967829,2	MCF-7	breast:
7	chr3:94934431..94935951-chr3:94936179..94938719,2	K562	blood:
8	chr3:94912857..94914770-chr3:94921596..94924370,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NSUN3-1	chr3:94890764-94891221	NONHSAT090744

Variant related genes	Relation type
RPS18P6	TF binding region
ENSG00000133316	chromatin interactions

Extended variants
information (count: 881 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:881 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529325318	chr3:94888765-94888766	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs549434025	chr3:94888779-94888780	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs377662014	chr3:94888786-94888787	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs369833865	chr3:94888798-94888799	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs185412697	chr3:94888817-94888818	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs72615787	chr3:94888821-94888822	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs190607869	chr3:94888862-94888863	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs570636664	chr3:94888865-94888866	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs539663808	chr3:94890163-94890164	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs557542139	chr3:94890804-94890805	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs574301125	chr3:94890808-94890809	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs6770382	chr3:94890828-94890829	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs553657615	chr3:94890836-94890837	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs149698983	chr3:94890839-94890840	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs573140907	chr3:94890854-94890855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs545427733	chr3:94890855-94890856	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs372136418	chr3:94890868-94890869	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs577788448	chr3:94890890-94890891	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs191418160	chr3:94890916-94890917	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs183626843	chr3:94890952-94890953	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs114758319	chr3:94890959-94890960	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs529105733	chr3:94890969-94890970	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs548981985	chr3:94890970-94890971	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs559630874	chr3:94891061-94891062	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs6779933	chr3:94891118-94891119	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs140454157	chr3:94891133-94891134	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs571264383	chr3:94891169-94891170	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs188559830	chr3:94891204-94891205	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs34639263	chr3:94891243-94891244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs34303506	chr3:94891249-94891250	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs4132577	chr3:94891307-94891308	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs547683036	chr3:94891320-94891321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs550717649	chr3:94891326-94891327	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs567738767	chr3:94891333-94891334	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs3905401	chr3:94891355-94891356	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs561683400	chr3:94891410-94891411	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs372576756	chr3:94891472-94891473	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs553381812	chr3:94891485-94891486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs573530476	chr3:94891546-94891547	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs538952390	chr3:94891558-94891559	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs558485005	chr3:94891590-94891591	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs575254171	chr3:94891595-94891596	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs529847593	chr3:94891613-94891614	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs56767894	chr3:94891661-94891662	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs561072516	chr3:94891693-94891694	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs73846929	chr3:94891772-94891773	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs35609810	chr3:94891788-94891789	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs369065262	chr3:94891803-94891804	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs542846316	chr3:94891812-94891813	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs559383971	chr3:94891834-94891835	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Oral cancer	21386901	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
Cancer	20164920	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	18458336	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
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:94891000-94892000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:94891200-94891800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:94891400-94891800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:94891400-94891800	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:94891400-94891800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:94891400-94891800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:94891600-94891800	Enhancers	Liver	Liver
8	chr3:94902800-94903800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:94919000-94919400	Enhancers	Liver	Liver
10	chr3:94923600-94924000	ZNF genes & repeats	Pancreas	Pancrea
11	chr3:94931000-94932200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:94931200-94932000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:94931600-94931800	Enhancers	Liver	Liver
14	chr3:94931800-94932200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:94931800-94932600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:94931800-94932600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr3:94931800-94936200	Weak transcription	Liver	Liver
18	chr3:94934400-94934600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:94934600-94935200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:94936200-94936400	Enhancers	Liver	Liver
21	chr3:94936400-94936800	Weak transcription	Liver	Liver
22	chr3:94936400-94937000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:94936600-94937200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr3:94936800-94937600	Enhancers	Liver	Liver
25	chr3:94937400-94937800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr3:94945600-94946600	Enhancers	Liver	Liver
27	chr3:94961200-94970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:94970400-94970600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:94970600-94971200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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