Variant report

Variant	nsv511863
Chromosome Location	chr6:29945557-29948665
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29941687..29943484-chr6:29948352..29949943,2	K562	blood:
2	chr6:29943871..29947343-chr6:29947953..29952410,7	K562	blood:
3	chr6:29855991..29858588-chr6:29944087..29945954,2	MCF-7	breast:
4	chr6:29944005..29947343-chr6:29947938..29951140,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-A-1	chr6:29945995-29946183	ENSG00000204625
2	lnc-HLA-A-1	chr6:29945995-29946177	NR_028032

Variant related genes	Relation type
ENSG00000230521	chromatin interactions
ENSG00000204625	chromatin interactions

Extended variants
information (count: 169 )
Associated
traits (count: 115 )

Variant overlapped rSNPs/rCNVs (count:169 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9260861	chr6:29945594-29945595	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs2246198	chr6:29945602-29945603	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs2246199	chr6:29945620-29945621	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs561461725	chr6:29945674-29945675	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs190867153	chr6:29945677-29945678	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs558148291	chr6:29945687-29945688	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs527357381	chr6:29945709-29945710	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs547174461	chr6:29945720-29945721	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs566945066	chr6:29945726-29945727	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs532888558	chr6:29945728-29945729	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs552572552	chr6:29945729-29945730	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs569311176	chr6:29945731-29945732	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs9260862	chr6:29945741-29945742	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs554976949	chr6:29945751-29945752	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs373282290	chr6:29945756-29945757	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs9260863	chr6:29945771-29945772	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs553115045	chr6:29945783-29945784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs56052612	chr6:29945802-29945803	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs368940129	chr6:29945804-29945805	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs115248111	chr6:29945830-29945831	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs9260864	chr6:29945841-29945842	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs371737599	chr6:29945861-29945862	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs9260865	chr6:29945898-29945899	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs369280683	chr6:29945911-29945912	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs376969779	chr6:29945930-29945931	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs3132685	chr6:29945949-29945950	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs183082108	chr6:29945956-29945957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs199833705	chr6:29945986-29945987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs371450230	chr6:29946011-29946012	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs386698652	chr6:29946019-29946020	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs112908929	chr6:29946020-29946021	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs9260867	chr6:29946021-29946022	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs202032807	chr6:29946022-29946023	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs561299092	chr6:29946044-29946045	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs374389679	chr6:29946049-29946050	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs73412367	chr6:29946064-29946065	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs572147619	chr6:29946077-29946078	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs201013880	chr6:29946093-29946094	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs115880913	chr6:29946107-29946108	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs375765529	chr6:29946124-29946125	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs9260868	chr6:29946157-29946158	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs371414455	chr6:29946167-29946168	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs111155355	chr6:29946184-29946185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs374162567	chr6:29946201-29946202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs370711292	chr6:29946248-29946249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs552772623	chr6:29946312-29946313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs563199778	chr6:29946313-29946314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs201089307	chr6:29946323-29946324	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs202096968	chr6:29946326-29946327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs386485018	chr6:29946377-29946378	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:115)

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
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Retinoblastoma	16790693	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	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
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	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
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Retinoblastoma	22278416	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Systemic lupus erythematosus	20877625	CNVD
Cleidocranial dysplasia	18696259	CNVD
Holoprosencephaly	21359414	CNVD
Liposarcoma	21253554	CNVD
Uveal melanoma	20484589	CNVD
Fibroblasts	20926602	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Pancreatic cancer	17952125	CNVD
Rett syndrome	21593744	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29944200-29945600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:29944400-29945600	Active TSS	Brain Anterior Caudate	brain
3	chr6:29944400-29945600	Active TSS	Stomach Smooth Muscle	stomach
4	chr6:29945000-29945600	Flanking Active TSS	Brain Cingulate Gyrus	brain
5	chr6:29945000-29945600	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr6:29945000-29945600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr6:29945000-29945600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:29945000-29945800	Bivalent Enhancer	Fetal Heart	heart
9	chr6:29945000-29945800	Flanking Active TSS	K562	blood
10	chr6:29945200-29945600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr6:29945200-29945600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:29945200-29945600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:29945200-29945600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:29945200-29945600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr6:29945200-29945600	Active TSS	Fetal Muscle Trunk	muscle
16	chr6:29945200-29945600	Bivalent Enhancer	Placenta	Placenta
17	chr6:29945200-29945600	Enhancers	Left Ventricle	heart
18	chr6:29945200-29945600	Enhancers	Pancreas	Pancrea
19	chr6:29945200-29945600	Enhancers	Stomach Mucosa	stomach
20	chr6:29945200-29945600	Flanking Active TSS	HepG2	liver
21	chr6:29945200-29945800	Enhancers	Liver	Liver
22	chr6:29945200-29948600	Weak transcription	Small Intestine	intestine
23	chr6:29945200-29948600	Weak transcription	Spleen	Spleen
24	chr6:29945400-29945600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:29945400-29945600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:29945400-29945600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:29945400-29945600	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:29945400-29945600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:29945400-29945600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:29945400-29945600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:29945400-29945600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:29945400-29945600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:29945400-29945600	Enhancers	Adipose Nuclei	Adipose
34	chr6:29945400-29945600	Enhancers	Brain Angular Gyrus	brain
35	chr6:29945400-29945600	Bivalent Enhancer	Brain Germinal Matrix	brain
36	chr6:29945400-29945600	Enhancers	Brain Hippocampus Middle	brain
37	chr6:29945400-29945600	Enhancers	Colon Smooth Muscle	Colon
38	chr6:29945400-29945600	Enhancers	Fetal Intestine Large	intestine
39	chr6:29945400-29945600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr6:29945400-29945600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr6:29945400-29945600	Enhancers	Rectal Smooth Muscle	rectum
42	chr6:29945400-29945600	Enhancers	Hela-S3	cervix
43	chr6:29945400-29945600	Enhancers	HMEC	breast
44	chr6:29945400-29945600	Enhancers	HUVEC	blood vessel
45	chr6:29945400-29945600	Enhancers	NHDF-Ad	bronchial
46	chr6:29945400-29945600	Enhancers	NHLF	lung
47	chr6:29945400-29945600	Enhancers	Osteobl	bone
48	chr6:29945400-29945800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr6:29945400-29945800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:29945400-29945800	Enhancers	Fetal Intestine Small	intestine

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