Variant report

Variant	esv16528
Chromosome Location	chr3:133969286-133969906
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	chr3:133969629-133969983	HepG2	liver:	n/a	n/a
2	BACH1	chr3:133969712-133970099	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr3:133969724-133969911	K562	blood:	n/a	n/a
4	BHLHE40	chr3:133969581-133969850	GM12878	blood:	n/a	chr3:133969655-133969671 chr3:133969583-133969599
5	BRCA1	chr3:133969713-133970025	Hela-S3	cervix:	n/a	n/a
6	CCNT2	chr3:133968957-133970062	K562	blood:	n/a	chr3:133969152-133969161
7	CEBPB	chr3:133969772-133970167	MCF-7	breast:	n/a	n/a
8	CEBPB	chr3:133969603-133970155	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr3:133969823-133970097	A549	lung:	n/a	n/a
10	CEBPB	chr3:133969792-133970177	IMR90	lung:	n/a	n/a
11	CEBPB	chr3:133969880-133970152	K562	blood:	n/a	n/a
12	CEBPB	chr3:133969818-133970104	HepG2	liver:	n/a	n/a
13	CEBPB	chr3:133969767-133970076	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr3:133969777-133970150	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPD	chr3:133969450-133969892	HepG2	liver:	n/a	n/a
16	CEBPD	chr3:133969102-133969411	HepG2	liver:	n/a	n/a
17	CHD2	chr3:133969729-133969945	HepG2	liver:	n/a	n/a
18	CHD2	chr3:133968678-133969977	Hela-S3	cervix:	n/a	chr3:133969153-133969163 chr3:133969235-133969245
19	CHD2	chr3:133969607-133969963	GM12878	blood:	n/a	n/a
20	CHD2	chr3:133968911-133969351	GM12878	blood:	n/a	chr3:133969153-133969163 chr3:133969235-133969245
21	CHD2	chr3:133969808-133969940	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr3:133969510-133969884	A549	lung:	n/a	n/a
23	CREB1	chr3:133969545-133969819	K562	blood:	n/a	n/a
24	CTCF	chr3:133969840-133969990	AG04449	skin:	n/a	n/a
25	CTCF	chr3:133969632-133969765	GM12878	blood:	n/a	n/a
26	CTCF	chr3:133969820-133969970	GM12869	blood:	n/a	n/a
27	CTCF	chr3:133969720-133969870	SAEC	small airway:	n/a	n/a
28	CTCF	chr3:133969620-133969770	AG04449	skin:	n/a	n/a
29	CTCF	chr3:133969617-133969748	Spleen_OC	spleen:	n/a	n/a
30	E2F1	chr3:133969573-133970073	Hela-S3	cervix:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969587-133969597 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
31	E2F4	chr3:133969613-133970090	MCF10A-Er-Src	breast:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
32	E2F4	chr3:133969690-133969904	GM12878	blood:	n/a	chr3:133969721-133969730
33	E2F6	chr3:133969632-133970031	K562	blood:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
34	E2F6	chr3:133969595-133970073	H1-hESC	embryonic stem cell:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
35	E2F6	chr3:133969560-133970229	H1-hESC	embryonic stem cell:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969587-133969597 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
36	E2F6	chr3:133969607-133970228	A549	lung:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
37	E2F6	chr3:133969669-133969838	K562	blood:	n/a	chr3:133969721-133969730
38	E2F6	chr3:133969614-133970016	K562	blood:	n/a	chr3:133969721-133969730 chr3:133969657-133969667 chr3:133969660-133969670 chr3:133969653-133969662 chr3:133969942-133969952
39	EBF1	chr3:133969610-133969904	GM12878	blood:	n/a	n/a
40	EBF1	chr3:133969718-133969841	GM12878	blood:	n/a	n/a
41	EGR1	chr3:133969499-133969798	GM12878	blood:	n/a	chr3:133969744-133969753 chr3:133969582-133969596 chr3:133969581-133969594 chr3:133969726-133969736 chr3:133969664-133969674
42	EGR1	chr3:133969263-133969401	GM12878	blood:	n/a	chr3:133969351-133969365
43	EGR1	chr3:133969445-133969768	GM12878	blood:	n/a	chr3:133969744-133969753 chr3:133969582-133969596 chr3:133969581-133969594 chr3:133969726-133969736 chr3:133969664-133969674
44	EGR1	chr3:133969213-133969437	GM12878	blood:	n/a	chr3:133969351-133969365
45	EGR1	chr3:133969491-133969791	K562	blood:	n/a	chr3:133969744-133969753 chr3:133969582-133969596 chr3:133969581-133969594 chr3:133969726-133969736 chr3:133969664-133969674
46	EGR1	chr3:133969520-133970012	GM12878	blood:	n/a	chr3:133969744-133969753 chr3:133969582-133969596 chr3:133969581-133969594 chr3:133969726-133969736 chr3:133969664-133969674
47	EGR1	chr3:133969473-133969809	K562	blood:	n/a	chr3:133969744-133969753 chr3:133969582-133969596 chr3:133969581-133969594 chr3:133969726-133969736 chr3:133969664-133969674
48	EGR1	chr3:133969187-133969415	K562	blood:	n/a	chr3:133969351-133969365
49	EGR1	chr3:133969246-133969458	K562	blood:	n/a	chr3:133969351-133969365
50	ELF1	chr3:133969036-133969381	K562	blood:	n/a	chr3:133969149-133969161 chr3:133969242-133969254

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:133969278-133969328	T-47D	breast:	n/a
2	chr3:133969278-133969328	GM12892	blood:	n/a
3	chr3:133969278-133969328	GM19239	blood:	n/a
4	chr3:133969278-133969328	AG09319	gingival:	n/a
5	chr3:133969591-133969641	PrEC	prostate:	n/a
6	chr3:133969278-133969328	NHDF-neo	bronchial:	n/a
7	chr3:133969591-133969641	HEK293	kidney:	embryo
8	chr3:133969591-133969641	SK-N-MC	brain:	n/a
9	chr3:133969591-133969641	HRPEpiC	eye:	n/a
10	chr3:133969278-133969328	PrEC	prostate:	n/a
11	chr3:133969591-133969641	AG04450	lung:	fetal
12	chr3:133969278-133969328	GM12891	blood:	n/a
13	chr3:133969591-133969641	GM06990	blood:	n/a
14	chr3:133969591-133969641	HCPEpiC	choroid plexus:	n/a
15	chr3:133969591-133969641	NHBE	bronchial:	n/a
16	chr3:133969278-133969328	SK-N-SH_RA	brain:	n/a
17	chr3:133969591-133969641	MCF10A-Er-Src	breast:	n/a
18	chr3:133969591-133969641	Jurkat	blood:	n/a
19	chr3:133969278-133969328	Caco-2	colon:	n/a
20	chr3:133969591-133969641	GM12878	blood:	n/a
21	chr3:133969591-133969641	BJ	skin:	n/a
22	chr3:133969278-133969328	NB4	blood:	n/a
23	chr3:133969591-133969641	HRCEpiC	kidney:	n/a
24	chr3:133969278-133969328	SK-N-MC	brain:	n/a
25	chr3:133969278-133969328	BE2_C	brain:	n/a
26	chr3:133969278-133969328	HMEC	breast:	n/a
27	chr3:133969591-133969641	HCF	heart:	n/a
28	chr3:133969278-133969328	HAEpiC	amniotic membrane:	n/a
29	chr3:133969278-133969328	AG09309	skin:	n/a
30	chr3:133969591-133969641	A549	lung:	n/a
31	chr3:133969591-133969641	NHDF-neo	bronchial:	n/a
32	chr3:133969278-133969328	NT2-D1	testis:	n/a
33	chr3:133969591-133969641	HEEpiC	esophagus:	n/a
34	chr3:133969591-133969641	HCM	heart:	n/a
35	chr3:133969591-133969641	IMR90	lung:	fetal
36	chr3:133969278-133969328	MCF10A-Er-Src	breast:	n/a
37	chr3:133969278-133969328	U87	brain:	n/a
38	chr3:133969591-133969641	SKMC	muscle:	n/a
39	chr3:133969278-133969328	NH-A	brain:	n/a
40	chr3:133969278-133969328	BJ	skin:	n/a
41	chr3:133969591-133969641	GM12891	blood:	n/a
42	chr3:133969591-133969641	ovcar-3	ovarian:	n/a
43	chr3:133969278-133969328	HCPEpiC	choroid plexus:	n/a
44	chr3:133969591-133969641	HepG2	liver:	n/a
45	chr3:133969278-133969328	PANC-1	pancreas:	n/a
46	chr3:133969591-133969641	HRE	kidney:	n/a
47	chr3:133969278-133969328	Jurkat	blood:	n/a
48	chr3:133969278-133969328	HRCEpiC	kidney:	n/a
49	chr3:133969591-133969641	BE2_C	brain:	n/a
50	chr3:133969278-133969328	AG04449	skin:	fetal

No.	Distal block	Cell Line	Cell type
1	chr3:133967562..133971327-chr3:134067822..134072418,4	MCF-7	breast:
2	chr12:102091137..102092560-chr3:133969061..133970004,4	Hela-S3	cervix:
3	chr3:133969194..133969719-chr3:136470769..136471350,2	Hela-S3	cervix:
4	chr3:133966982..133969357-chr3:134203200..134205519,3	MCF-7	breast:
5	chr3:133969091..133969747-chr7:35839773..35840580,2	Hela-S3	cervix:
6	chr3:133969854..133971498-chr3:134203715..134206373,2	K562	blood:
7	chr3:133969506..133971460-chr3:134202147..134204798,2	K562	blood:
8	chr12:15942011..15942548-chr3:133969611..133970273,2	Hela-S3	cervix:
9	chr3:133968058..133969986-chr3:134093152..134094854,2	MCF-7	breast:
10	chr3:22413816..22414336-chr3:133969155..133969870,2	HCT-116	colon:
11	chr3:133969851..133972992-chr3:133976680..133979913,3	K562	blood:
12	chr3:133969328..133972317-chr3:134030794..134032589,3	MCF-7	breast:
13	chr19:10206614..10207226-chr3:133969204..133969782,2	NB4	blood:

Variant related genes	Relation type
RYK	TF binding region
RYK	CpG island
ENSG00000122545	chromatin interactions
ENSG00000129055	chromatin interactions
ENSG00000260633	chromatin interactions
ENSG00000151491	chromatin interactions
ENSG00000111666	chromatin interactions
ENSG00000118007	chromatin interactions
ENSG00000182923	chromatin interactions
ENSG00000228878	chromatin interactions
ENSG00000130812	chromatin interactions
ENSG00000214289	chromatin interactions
ENSG00000240006	chromatin interactions
ENSG00000114019	chromatin interactions
ENSG00000151789	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564758389	chr3:133969342-133969343	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
2	rs201505334	chr3:133969348-133969349	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
3	rs139860270	chr3:133969352-133969353	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
4	rs567577474	chr3:133969356-133969357	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
5	rs536406334	chr3:133969357-133969358	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
6	rs550024418	chr3:133969427-133969428	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
7	rs587770426	chr3:133969437-133969438	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
8	rs368961042	chr3:133969438-133969439	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
9	rs587744425	chr3:133969487-133969488	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
10	rs570101510	chr3:133969592-133969593	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
11	rs200139418	chr3:133969656-133969657	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
12	rs538792529	chr3:133969704-133969705	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
13	rs565684423	chr3:133969715-133969716	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	14 gene(s)	Overlapped CNVs	n/a
14	rs112646711	chr3:133969770-133969771	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
15	rs528322332	chr3:133969786-133969787	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
16	rs558888515	chr3:133969793-133969794	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
17	rs572396877	chr3:133969805-133969806	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
18	rs372446678	chr3:133969815-133969816	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
19	rs374302260	chr3:133969901-133969902	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
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
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
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	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
Intracranial aneurysm	16715129	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Myelofibrosis	22110671	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Non-syndromic sensorineural hearing loss	22297974	CNVD

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133966600-133970200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:133967400-133970400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:133967600-133970200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:133967800-133969800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:133967800-133970000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:133967800-133970200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:133967800-133970200	Active TSS	A549	lung
8	chr3:133968000-133970000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:133968000-133970200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:133968000-133970200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:133968000-133970200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:133968000-133970200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:133968000-133970200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:133968000-133970200	Active TSS	Fetal Intestine Small	intestine
15	chr3:133968000-133970200	Active TSS	Hela-S3	cervix
16	chr3:133968000-133970200	Active TSS	HSMMtube	muscle
17	chr3:133968000-133970200	Active TSS	K562	blood
18	chr3:133968000-133970400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:133968000-133970400	Active TSS	HepG2	liver
20	chr3:133968000-133970800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:133968200-133969800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr3:133968200-133970000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:133968200-133970000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:133968200-133970000	Active TSS	NHEK	skin
25	chr3:133968200-133970200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr3:133968200-133970200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:133968200-133970200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:133968200-133970200	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr3:133968200-133970200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:133968200-133970200	Active TSS	Aorta	Aorta
31	chr3:133968200-133970200	Active TSS	Brain Angular Gyrus	brain
32	chr3:133968200-133970200	Active TSS	Fetal Intestine Large	intestine
33	chr3:133968200-133970200	Active TSS	Fetal Thymus	thymus
34	chr3:133968200-133970200	Active TSS	Ovary	ovary
35	chr3:133968200-133970200	Active TSS	Psoas Muscle	Psoas
36	chr3:133968200-133970200	Active TSS	HMEC	breast
37	chr3:133968200-133970200	Active TSS	HSMM	muscle
38	chr3:133968200-133970200	Active TSS	NHDF-Ad	bronchial
39	chr3:133968200-133970600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:133968200-133970800	Active TSS	Right Ventricle	heart
41	chr3:133968400-133970000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:133968400-133970000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:133968400-133970000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:133968400-133970000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:133968400-133970000	Active TSS	Esophagus	oesophagus
46	chr3:133968400-133970000	Active TSS	NHLF	lung
47	chr3:133968400-133970200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:133968400-133970200	Active TSS	Colonic Mucosa	Colon
49	chr3:133968400-133970200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:133968400-133970200	Active TSS	Fetal Muscle Trunk	muscle

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