Variant report

Variant	nsv823700
Chromosome Location	chr6:54709648-54710116
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	POLR2A	chr6:54709547-54709894	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
2	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
3	chr20:52738859..52741782-chr6:54708785..54710307,2	MCF-7	breast:
4	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:
5	chr6:54483454..54486448-chr6:54709404..54710933,2	MCF-7	breast:

Variant related genes	Relation type
FAM83B	TF binding region
ENSG00000224984	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 79 )

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	rs4712075	chr6:54709692-54709693	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs548807228	chr6:54709721-54709722	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs568711574	chr6:54709754-54709755	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
4	rs78507379	chr6:54709759-54709760	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs572127750	chr6:54709791-54709792	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs4715485	chr6:54709795-54709796	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs12194012	chr6:54709851-54709852	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs182183760	chr6:54709867-54709868	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs12207559	chr6:54709868-54709869	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs541961200	chr6:54709878-54709879	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs555142997	chr6:54709883-54709884	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs374812312	chr6:54709886-54709887	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs1503133	chr6:54709911-54709912	Weak transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs12216039	chr6:54709922-54709923	Weak transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs552384736	chr6:54709944-54709945	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs564057502	chr6:54709955-54709956	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs532818897	chr6:54709962-54709963	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs532911708	chr6:54709964-54709965	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs12216049	chr6:54709969-54709970	Weak transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs563353350	chr6:54709986-54709987	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs187155056	chr6:54709990-54709991	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs368277027	chr6:54709992-54709993	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs549146198	chr6:54710008-54710009	Weak transcription Bivalent/Poised TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs12195438	chr6:54710030-54710031	Weak transcription Bivalent/Poised TSS Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs145021458	chr6:54710041-54710042	Weak transcription Bivalent/Poised TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs151023089	chr6:54710065-54710066	Weak transcription Bivalent/Poised TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs17682328	chr6:54710076-54710077	Weak transcription Bivalent/Poised TSS Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:79)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	20164919	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54707200-54710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54707400-54710200	Weak transcription	NHEK	skin
3	chr6:54707400-54710800	Weak transcription	Placenta	Placenta
4	chr6:54709000-54710000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:54709000-54710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:54709200-54709800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:54709200-54710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54709200-54710200	Enhancers	HMEC	breast
11	chr6:54709400-54709800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr6:54709400-54710800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:54709600-54709800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:54709800-54710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:54710000-54710400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
17	chr6:54710000-54710600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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