Variant report

Variant	esv3473876
Chromosome Location	chr6:29819114-29819949
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:26189787..26191477-chr6:29817931..29819451,2	MCF-7	breast:
2	chr6:29819155..29821772-chr6:29909018..29911343,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206503	chromatin interactions
ENSG00000227195	chromatin interactions
ENSG00000227766	chromatin interactions

Extended variants
information (count: 55 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:55 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs560400725	chr6:29819179-29819180	Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs190119653	chr6:29819180-29819181	Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs2523758	chr6:29819198-29819199	Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs2975035	chr6:29819202-29819203	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs139334314	chr6:29819204-29819205	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs571804888	chr6:29819206-29819207	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs145181863	chr6:29819212-29819213	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs9258584	chr6:29819222-29819223	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs113222838	chr6:29819226-29819227	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs533650568	chr6:29819232-29819233	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs187652090	chr6:29819248-29819249	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs144450403	chr6:29819252-29819253	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs543671428	chr6:29819254-29819255	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs9258585	chr6:29819280-29819281	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs12528253	chr6:29819281-29819282	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs538129349	chr6:29819285-29819286	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs368485835	chr6:29819301-29819302	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs371355448	chr6:29819309-29819310	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs547613110	chr6:29819324-29819325	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs2517869	chr6:29819325-29819326	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs62392525	chr6:29819330-29819331	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs2517868	chr6:29819338-29819339	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs72845918	chr6:29819375-29819376	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs9258588	chr6:29819431-29819432	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs546046504	chr6:29819446-29819447	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs2107199	chr6:29819475-29819476	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs3998725	chr6:29819489-29819490	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs140199815	chr6:29819527-29819528	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs561726355	chr6:29819539-29819540	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs7451408	chr6:29819541-29819542	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs546980618	chr6:29819546-29819547	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs1317834	chr6:29819554-29819555	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs532842545	chr6:29819563-29819564	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs143978289	chr6:29819573-29819574	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs368161138	chr6:29819598-29819599	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs9258593	chr6:29819599-29819600	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs192770185	chr6:29819600-29819601	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs386698494	chr6:29819601-29819602	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs114088589	chr6:29819602-29819603	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
40	rs115047714	chr6:29819603-29819604	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs3880454	chr6:29819648-29819649	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs2107198	chr6:29819662-29819663	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs144878463	chr6:29819687-29819688	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs2107197	chr6:29819694-29819695	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs7451468	chr6:29819695-29819696	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs3892860	chr6:29819741-29819742	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs542002925	chr6:29819761-29819762	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs73747788	chr6:29819782-29819783	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs2428509	chr6:29819813-29819814	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs540655679	chr6:29819851-29819852	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:104)

Disease	PMID	Source
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
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Ewing''s sarcoma	17952124	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	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
Ovarian cancer	21781307	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
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
Chronic lymphocytic leukemia	21546498	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	17133270	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Breast cancer	22032731	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Retinoblastoma	16790693	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
T-cell lymphomas	19863542	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18765545	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	19571809	CNVD
Schizophrenia	19571808	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
abnormal development	18461090	CNVD
Breast cancer	21509527	CNVD
Melanoma	17363583	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29818400-29820600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29818400-29823600	Weak transcription	Right Atrium	heart
3	chr6:29819000-29819200	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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