Variant report

Variant	esv2088436
Chromosome Location	chr6:30886257-30886768
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	chr6:30886552-30886581	K562	blood:	n/a	n/a
2	TAL1	chr6:30886495-30886685	K562	blood:	n/a	n/a
3	TEAD4	chr6:30886377-30886838	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30851061..30852670-chr6:30885316..30887287,2	MCF-7	breast:
2	chr6:30882042..30885135-chr6:30886350..30889389,4	MCF-7	breast:
3	chr6:30881968..30885056-chr6:30885339..30888267,3	MCF-7	breast:
4	chr6:30874031..30876407-chr6:30886352..30887855,2	MCF-7	breast:

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000213780	chromatin interactions
ENSG00000204580	chromatin interactions
ENSG00000264731	chromatin interactions
ENSG00000137411	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 122 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9262293	chr6:30886350-30886351	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs576233866	chr6:30886353-30886354	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs542371741	chr6:30886525-30886526	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs142823593	chr6:30886551-30886552	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs201161091	chr6:30886568-30886569	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs190268810	chr6:30886629-30886630	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs572473514	chr6:30886641-30886642	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs541091465	chr6:30886659-30886660	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs199628912	chr6:30886665-30886666	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs564457017	chr6:30886677-30886678	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs142164262	chr6:30886682-30886683	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs151183326	chr6:30886683-30886684	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs375719143	chr6:30886701-30886702	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs200200291	chr6:30886707-30886708	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs563526313	chr6:30886715-30886716	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs529087730	chr6:30886719-30886720	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs115947485	chr6:30886724-30886725	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs41273021	chr6:30886729-30886730	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	mRNA abundance
19	rs146126712	chr6:30886730-30886731	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:122)

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
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
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
Autism	22495311	CNVD
Cancer	16790693	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21785460	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	19571808	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
abnormal development	18461090	CNVD
Melanoma	17363583	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
Breast cancer	21364760	CNVD
Lung cancer	21569311	CNVD
Systemic lupus erythematosus	19279649	CNVD
Retinoblastoma	16790693	CNVD
Acute myocardial infarction	18032375	CNVD
Renal cell carcinoma	19150565	CNVD
Systemic lupus erythematosus	19591781	CNVD
Attention deficit hyperactivity disorder	19287146	CNVD
Autism	19287146	CNVD
Erythema nodosum in leprosy	19287146	CNVD
Henoch-schoenlein purpura	19287146	CNVD
Liver cirrhosis	19287146	CNVD
Systemic lupus erythematosus	19287146	CNVD
Congenital adrenal hyperplasia	18478071	CNVD
Systemic lupus erythematosus	19287147	CNVD
Osteosarcoma	16790693	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30882600-30886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:30882800-30890200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:30882800-30890200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:30883000-30889000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:30883200-30888400	Weak transcription	Small Intestine	intestine
6	chr6:30883400-30887400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:30883400-30887400	Weak transcription	HSMMtube	muscle
8	chr6:30883400-30891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:30883400-30894400	Weak transcription	Hela-S3	cervix
10	chr6:30883400-30895800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:30883400-30897000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:30883600-30890800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:30883600-30892000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:30883800-30886600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:30883800-30887400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:30883800-30889800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:30883800-30889800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:30883800-30890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:30883800-30890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:30883800-30894000	Weak transcription	Fetal Kidney	kidney
21	chr6:30883800-30894200	Weak transcription	Psoas Muscle	Psoas
22	chr6:30883800-30895200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:30883800-30895800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:30883800-30896600	Strong transcription	Fetal Muscle Leg	muscle
25	chr6:30884000-30888200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:30884000-30888400	Weak transcription	NHDF-Ad	bronchial
27	chr6:30884000-30889600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30884000-30889600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:30884000-30890000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:30884000-30890200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr6:30884000-30891600	Strong transcription	Colon Smooth Muscle	Colon
32	chr6:30884000-30894800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr6:30884000-30894800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:30884000-30895000	Strong transcription	Placenta	Placenta
35	chr6:30884000-30895800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:30884000-30896000	Strong transcription	Fetal Stomach	stomach
37	chr6:30884000-30896200	Strong transcription	Fetal Thymus	thymus
38	chr6:30884000-30897000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:30884200-30889800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:30884200-30893800	Weak transcription	Fetal Brain Male	brain
41	chr6:30884200-30894000	Weak transcription	HSMM	muscle
42	chr6:30884200-30894800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr6:30884200-30894800	Strong transcription	Fetal Intestine Large	intestine
44	chr6:30884200-30895000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:30884200-30895400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:30884200-30895600	Strong transcription	Fetal Intestine Small	intestine
47	chr6:30884200-30896200	Strong transcription	Fetal Brain Female	brain
48	chr6:30884400-30886400	Strong transcription	A549	lung
49	chr6:30884400-30887400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:30884400-30890400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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