Variant report

Variant	nsv934119
Chromosome Location	chr11:17542691-17548601
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	BHLHE40	chr11:17545637-17545681	HepG2	liver:	n/a	n/a
2	CEBPB	chr11:17545610-17545814	A549	lung:	n/a	n/a
3	CEBPB	chr11:17545613-17545931	HepG2	liver:	n/a	n/a
4	CTCF	chr11:17547960-17548110	BE2_C	brain:	n/a	n/a
5	MAFK	chr11:17545247-17545381	HepG2	liver:	n/a	chr11:17545285-17545299 chr11:17545286-17545301
6	MAFK	chr11:17545207-17545432	HepG2	liver:	n/a	chr11:17545285-17545299 chr11:17545286-17545301
7	POLR2A	chr11:17545632-17545669	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:17545594-17545599	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17404201..17406453-chr11:17548482..17550709,2	K562	blood:
2	chr11:17408865..17412169-chr11:17547784..17549963,3	K562	blood:
3	chr11:17538690..17542408-chr11:17546927..17550590,3	MCF-7	breast:
4	chr11:17401047..17402845-chr11:17547923..17549749,2	MCF-7	breast:

Variant related genes	Relation type
USH1C	TF binding region
ENSG00000260196	chromatin interactions
ENSG00000187486	chromatin interactions

Extended variants
information (count: 314 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:314 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558561478	chr11:17542695-17542696	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs74695229	chr11:17542703-17542704	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs57959744	chr11:17542720-17542721	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs556481348	chr11:17542721-17542722	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs551090498	chr11:17542723-17542724	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190422899	chr11:17542774-17542775	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs183569061	chr11:17542783-17542784	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs188049377	chr11:17542867-17542868	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs573328148	chr11:17542871-17542872	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs2240488	chr11:17542872-17542873	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs368988911	chr11:17542874-17542875	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs199960136	chr11:17542880-17542881	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs532357891	chr11:17542881-17542882	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs140934960	chr11:17542909-17542910	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs144896074	chr11:17542938-17542939	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567436989	chr11:17542957-17542958	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs147956944	chr11:17542960-17542961	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs191271622	chr11:17542988-17542989	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs146119431	chr11:17543000-17543001	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs548719572	chr11:17543046-17543047	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs566940973	chr11:17543060-17543061	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs573613890	chr11:17543105-17543106	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs527425273	chr11:17543109-17543110	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs368722765	chr11:17543116-17543117	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs551962689	chr11:17543136-17543137	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs570495534	chr11:17543140-17543141	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs140145430	chr11:17543161-17543162	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs182590232	chr11:17543168-17543169	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs568314712	chr11:17543197-17543198	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs16934376	chr11:17543203-17543204	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs534576032	chr11:17543205-17543206	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs186789097	chr11:17543220-17543221	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs370353490	chr11:17543237-17543238	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs540757459	chr11:17543242-17543243	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs558594077	chr11:17543298-17543299	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs35564438	chr11:17543312-17543313	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs546865110	chr11:17543327-17543328	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs576851364	chr11:17543341-17543342	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs544156203	chr11:17543432-17543433	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs562848314	chr11:17543466-17543467	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs530363477	chr11:17543470-17543471	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs542153560	chr11:17543487-17543488	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs55830019	chr11:17543490-17543491	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs560763319	chr11:17543501-17543502	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs527865261	chr11:17543511-17543512	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs376043185	chr11:17543532-17543533	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs564141821	chr11:17543571-17543572	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs531335317	chr11:17543601-17543602	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144034703	chr11:17543610-17543611	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs150949220	chr11:17543626-17543627	Weak transcription Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Cancer	21183584	CNVD
Gastric adenocarcinoma	19115996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	19759907	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Thyroid cancer	19087340	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Parathyroid adenoma	22454399	CNVD
Chordoma	21602918	CNVD
Breast cancer	21949216	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	19222835	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Beckwith-Wiedemann syndrome	21518781	CNVD
Wilms tumour	21518781	CNVD
Hepatoblastoma	21518781	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Gastric cancer	17908304	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	20724749	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Autism	22495311	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Multiple myeloma	16461302	CNVD
Non-small cell lung cancer	21385341	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21858162	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	21899760	CNVD
Lung adenocarcinoma	17086460	CNVD
Urothelial cell carcinoma	18451213	CNVD
Lung cancer	17086460	CNVD
Uterine serous papillary cancer	19536090	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Medulloblastoma	16783165	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
2	chr11:17527600-17549200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:17528800-17544000	Weak transcription	Gastric	stomach
4	chr11:17529800-17548600	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr11:17531600-17547200	Strong transcription	Fetal Intestine Large	intestine
6	chr11:17531800-17552400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:17532200-17547200	Strong transcription	Fetal Intestine Small	intestine
8	chr11:17537400-17544800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:17537400-17546800	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:17538400-17562200	Weak transcription	Small Intestine	intestine
11	chr11:17539600-17550000	Weak transcription	Spleen	Spleen
12	chr11:17540800-17552400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:17541000-17552600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr11:17541400-17548000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:17541400-17552400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:17541600-17549600	Weak transcription	Brain Anterior Caudate	brain
17	chr11:17541600-17550000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:17541600-17551600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr11:17541600-17555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:17542000-17544000	Weak transcription	Colonic Mucosa	Colon
21	chr11:17542000-17544200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:17542000-17547800	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:17542000-17548000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:17542400-17543200	Enhancers	NHEK	skin
25	chr11:17542400-17544000	Weak transcription	Fetal Stomach	stomach
26	chr11:17542400-17547800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:17542600-17543400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:17542600-17549400	Weak transcription	Brain Angular Gyrus	brain
29	chr11:17542600-17550000	Weak transcription	Brain Substantia Nigra	brain
30	chr11:17543200-17543400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:17544000-17545400	Strong transcription	Gastric	stomach
32	chr11:17544000-17549800	Strong transcription	Colonic Mucosa	Colon
33	chr11:17544200-17548000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:17544600-17545200	Strong transcription	Fetal Stomach	stomach
35	chr11:17545200-17547400	Weak transcription	Fetal Stomach	stomach
36	chr11:17545400-17553000	Weak transcription	Gastric	stomach
37	chr11:17545800-17550000	Weak transcription	Right Atrium	heart
38	chr11:17546800-17550000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:17547200-17550400	Genic enhancers	Fetal Intestine Large	intestine
40	chr11:17547200-17563200	Genic enhancers	Fetal Intestine Small	intestine
41	chr11:17547800-17548000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:17547800-17548000	Enhancers	HSMMtube	muscle
43	chr11:17547800-17548400	Enhancers	Brain Hippocampus Middle	brain
44	chr11:17547800-17548400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr11:17547800-17548400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr11:17547800-17548600	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr11:17548000-17548200	Enhancers	Brain Cingulate Gyrus	brain
48	chr11:17548000-17548400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr11:17548000-17548400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:17548000-17550000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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