Variant report

Variant	esv12148
Chromosome Location	chr6:5112412-5112918
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	EP300	chr6:5112666-5113074	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr6:5112692-5113062	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr6:5112470-5113301	SK-N-SH	brain:	n/a	n/a
4	FOS	chr6:5112755-5113055	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:5112868-5112992	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr6:5112766-5112913	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr6:5112518-5113274	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr6:5112670-5113153	A549	lung:	n/a	n/a
9	GATA3	chr6:5112595-5113222	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr6:5112539-5113318	SK-N-SH	brain:	n/a	n/a
11	JUND	chr6:5112385-5113258	SK-N-SH	brain:	n/a	n/a
12	JUND	chr6:5112578-5113207	SK-N-SH	brain:	n/a	n/a
13	MAFF	chr6:5112784-5112786	K562	blood:	n/a	n/a
14	MAX	chr6:5112648-5113195	SK-N-SH	brain:	n/a	n/a
15	MAX	chr6:5112695-5113145	SK-N-SH	brain:	n/a	n/a
16	MAX	chr6:5112627-5113209	A549	lung:	n/a	n/a
17	MYC	chr6:5112695-5113043	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr6:5112756-5112966	MCF10A-Er-Src	breast:	n/a	n/a
19	NFIC	chr6:5112532-5113140	SK-N-SH	brain:	n/a	n/a
20	NR3C1	chr6:5112542-5113092	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
21	NR3C1	chr6:5112677-5113080	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
22	NR3C1	chr6:5112685-5112966	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
23	NR3C1	chr6:5112706-5112877	A549	lung:	n/a	n/a
24	NR3C1	chr6:5112642-5112992	A549	lung:	n/a	chr6:5112703-5112729 chr6:5112703-5112729
25	PBX3	chr6:5112520-5113217	SK-N-SH	brain:	n/a	n/a
26	PBX3	chr6:5112483-5113328	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:5112359-5112638	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:5112662-5113088	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr6:5112808-5112968	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr6:5112774-5112811	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:5112696-5112722	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:5112751-5112772	HepG2	liver:	n/a	n/a
33	RCOR1	chr6:5112592-5113315	IMR90	lung:	n/a	n/a
34	REST	chr6:5112805-5113099	SK-N-SH	brain:	n/a	n/a
35	TCF12	chr6:5112470-5113290	SK-N-SH	brain:	n/a	n/a
36	TCF12	chr6:5112432-5113244	SK-N-SH	brain:	n/a	n/a
37	TEAD4	chr6:5112598-5113224	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LYRM4	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs364857	chr6:5112427-5112428	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs115832614	chr6:5112435-5112436	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs75569561	chr6:5112449-5112450	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs393332	chr6:5112465-5112466	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs411483	chr6:5112499-5112500	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs183977647	chr6:5112530-5112531	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs551078305	chr6:5112561-5112562	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs146343563	chr6:5112572-5112573	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs591481	chr6:5112576-5112577	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs139067968	chr6:5112584-5112585	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs578211383	chr6:5112593-5112594	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs142842282	chr6:5112601-5112602	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs17139442	chr6:5112614-5112615	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs528445097	chr6:5112615-5112616	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs545724927	chr6:5112622-5112623	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs143730602	chr6:5112631-5112632	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs144189510	chr6:5112658-5112659	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs543018099	chr6:5112672-5112673	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs57697533	chr6:5112712-5112713	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs394252	chr6:5112747-5112748	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs441482	chr6:5112814-5112815	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs189163286	chr6:5112835-5112836	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs541710438	chr6:5112845-5112846	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs441463	chr6:5112853-5112854	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs115015200	chr6:5112862-5112863	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs379508	chr6:5112912-5112913	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs379511	chr6:5112916-5112917	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:98)

Disease	PMID	Source
Developmental delay	19490664	CNVD
Cancer	21183584	CNVD
Multiple Epiphyseal Dysplasia	20877625	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Glaucoma	18694899	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Cancer	20164920	CNVD
Colorectal cancer	21297112	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Myelodysplastic syndrome	21251322	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
Autism	22495311	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Breast cancer	22844521	CNVD
HIV/AIDS	22844521	CNVD
Ovarian cancer	22844521	CNVD
Prostate cancer	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21552322	CNVD
Immune disease	21076436	CNVD
Autoimmune disease	19135723	CNVD
Systemic lupus erythematosus	17953491	CNVD
Recurrent Infections	22737222	CNVD
Systemic lupus erythematosus	21904924	CNVD
Ependymoma	19289631	CNVD
small cell lung cancer	20016488	CNVD
Gestational infection	22844521	CNVD
Head circumference	22844521	CNVD
Infertility	22844521	CNVD
Recurrent birth weight diabetes	22844521	CNVD
Obesity	22844521	CNVD
Recurrent pregnancy loss	22844521	CNVD
Intellectual disability	21811512	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
dysmorphism	22105932	CNVD
psychomotor delay	22105932	CNVD
Ovarian cancer	19193619	CNVD
Osteosarcoma	16790693	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Amyotrophic lateral sclerosis	20685689	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5097600-5112800	Weak transcription	K562	blood
3	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
4	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:5103200-5114000	Weak transcription	Dnd41	blood
9	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:5105000-5113200	Strong transcription	HepG2	liver
11	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:5105800-5125600	Weak transcription	Ovary	ovary
14	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
15	chr6:5107200-5112600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
17	chr6:5108000-5113600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:5108200-5112800	Strong transcription	Spleen	Spleen
19	chr6:5109000-5113800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:5109000-5116400	Weak transcription	Brain Germinal Matrix	brain
21	chr6:5109200-5118600	Weak transcription	Esophagus	oesophagus
22	chr6:5109200-5121800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:5109200-5130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:5109400-5121600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:5109800-5113800	Weak transcription	Colonic Mucosa	Colon
26	chr6:5110000-5114000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:5110200-5113000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:5110200-5121800	Weak transcription	Brain Anterior Caudate	brain
29	chr6:5110400-5121600	Weak transcription	Adipose Nuclei	Adipose
30	chr6:5110600-5112600	Strong transcription	Lung	lung
31	chr6:5110600-5112800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:5110600-5113800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:5111200-5119200	Weak transcription	Fetal Intestine Large	intestine
34	chr6:5111600-5112800	Enhancers	Right Ventricle	heart
35	chr6:5111600-5113000	Strong transcription	Gastric	stomach
36	chr6:5111600-5113200	Enhancers	Fetal Heart	heart
37	chr6:5111600-5113200	Enhancers	Left Ventricle	heart
38	chr6:5111600-5113600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:5111600-5113600	Strong transcription	Fetal Intestine Small	intestine
40	chr6:5111800-5112600	Genic enhancers	NHEK	skin
41	chr6:5111800-5113000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr6:5111800-5113000	Enhancers	Fetal Thymus	thymus
43	chr6:5111800-5113200	Genic enhancers	Fetal Stomach	stomach
44	chr6:5111800-5113400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr6:5111800-5113800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:5112000-5112800	Genic enhancers	Right Atrium	heart
47	chr6:5112000-5113400	Enhancers	NHDF-Ad	bronchial
48	chr6:5112000-5113600	Enhancers	HMEC	breast
49	chr6:5112000-5114000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:5112200-5112600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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