Variant report

Variant	esv1793167
Chromosome Location	chr6:49459978-49466686
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr6:49464896-49465604	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr6:49464987-49465434	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr6:49465026-49465421	ECC-1	luminal epithelium:	n/a	n/a
4	FOXA1	chr6:49465046-49465385	ECC-1	luminal epithelium:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
5	FOXA1	chr6:49464977-49465460	ECC-1	luminal epithelium:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
6	FOXA1	chr6:49465044-49465404	T-47D	breast:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
7	FOXA1	chr6:49465005-49465267	T-47D	breast:	n/a	chr6:49465247-49465262 chr6:49465213-49465225
8	FOXM1	chr6:49464868-49465588	ECC-1	luminal epithelium:	n/a	n/a
9	MAFF	chr6:49464846-49465092	HepG2	liver:	n/a	chr6:49464961-49464979
10	MAFK	chr6:49464847-49465078	HepG2	liver:	n/a	n/a
11	MAFK	chr6:49464899-49465092	HepG2	liver:	n/a	n/a
12	NFIC	chr6:49464954-49465529	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr6:49464941-49465621	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr6:49462316-49462914	K562	blood:	n/a	n/a
15	POLR2A	chr6:49462750-49462769	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:49463592-49463747	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:49466667-49466718	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr6:49461849-49462939	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:49462218-49464476	K562	blood:	n/a	n/a
20	TBL1XR1	chr6:49465981-49466000	K562	blood:	n/a	n/a
21	TCF12	chr6:49464991-49465576	ECC-1	luminal epithelium:	n/a	n/a
22	TCF12	chr6:49464839-49465566	ECC-1	luminal epithelium:	n/a	n/a
23	TEAD4	chr6:49464942-49465471	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr6:49464910-49465559	ECC-1	luminal epithelium:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:49460031-49460081	MCF-7	breast:	n/a
2	chr6:49466300-49466350	NH-A	brain:	n/a
3	chr6:49460031-49460081	NHBE	bronchial:	n/a
4	chr6:49460031-49460081	SAEC	small airway:	n/a
5	chr6:49460031-49460081	GM12891	blood:	n/a
6	chr6:49460031-49460081	CMK	blood:	n/a
7	chr6:49460031-49460081	HCF	heart:	n/a
8	chr6:49466300-49466350	MCF-7	breast:	n/a
9	chr6:49466300-49466350	BE2_C	brain:	n/a
10	chr6:49460031-49460081	PANC-1	pancreas:	n/a
11	chr6:49460031-49460081	HRE	kidney:	n/a
12	chr6:49466300-49466350	HEEpiC	esophagus:	n/a
13	chr6:49466300-49466350	HEK293	kidney:	embryo
14	chr6:49460031-49460081	GM19239	blood:	n/a
15	chr6:49460031-49460081	AG09319	gingival:	n/a
16	chr6:49460031-49460081	ovcar-3	ovarian:	n/a
17	chr6:49466300-49466350	Caco-2	colon:	n/a
18	chr6:49460031-49460081	HMEC	breast:	n/a
19	chr6:49466300-49466350	PFSK-1	brain:	n/a
20	chr6:49460031-49460081	RPTEC	kidney:	n/a
21	chr6:49460031-49460081	PFSK-1	brain:	n/a
22	chr6:49460031-49460081	HCM	heart:	n/a
23	chr6:49466300-49466350	RPTEC	kidney:	n/a
24	chr6:49466300-49466350	HRE	kidney:	n/a
25	chr6:49466300-49466350	CMK	blood:	n/a
26	chr6:49466300-49466350	Hela-S3	cervix:	n/a
27	chr6:49460031-49460081	AG04450	lung:	fetal
28	chr6:49466300-49466350	HRCEpiC	kidney:	n/a
29	chr6:49460031-49460081	HUVEC	blood vessel:	n/a
30	chr6:49466300-49466350	PrEC	prostate:	n/a
31	chr6:49466300-49466350	AG09309	skin:	n/a
32	chr6:49460031-49460081	HEK293	kidney:	embryo
33	chr6:49466300-49466350	ProgFib	skin:	n/a
34	chr6:49460031-49460081	HIPEpiC	eye:	n/a
35	chr6:49466300-49466350	H1-hESC	embryonic stem cell:	embryo
36	chr6:49466300-49466350	T-47D	breast:	n/a
37	chr6:49466300-49466350	AG09319	gingival:	n/a
38	chr6:49460031-49460081	ECC-1	luminal epithelium:	n/a
39	chr6:49460031-49460081	Jurkat	blood:	n/a
40	chr6:49460031-49460081	AG09309	skin:	n/a
41	chr6:49466300-49466350	K562	blood:	n/a
42	chr6:49460031-49460081	K562	blood:	n/a
43	chr6:49466300-49466350	HRPEpiC	eye:	n/a
44	chr6:49466300-49466350	HPAEpiC	pulmonary alveolar:	n/a
45	chr6:49460031-49460081	BE2_C	brain:	n/a
46	chr6:49466300-49466350	GM06990	blood:	n/a
47	chr6:49466300-49466350	HCPEpiC	choroid plexus:	n/a
48	chr6:49466300-49466350	GM12892	blood:	n/a
49	chr6:49460031-49460081	NHDF-neo	bronchial:	n/a
50	chr6:49460031-49460081	LNCaP	prostate:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:49458471..49460387-chr6:49460980..49463015,2	K562	blood:
2	chr6:49431721..49433516-chr6:49458650..49460317,2	K562	blood:
3	chr6:49429806..49431359-chr6:49457434..49460019,2	K562	blood:
4	chr6:49460315..49462517-chr6:49463838..49466982,4	K562	blood:
5	chr6:49458471..49460387-chr6:49460980..49463015,2	K562	blood:
6	chr6:49460315..49462517-chr6:49463838..49466982,4	K562	blood:

No data

Variant related genes	Relation type
GLYATL3	TF binding region
GLYATL3	CpG island
ENSG00000031691	chromatin interactions
ENSG00000146085	chromatin interactions

Extended variants
information (count: 214 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:214 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2501968	chr6:49459978-49459979	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs568913239	chr6:49459989-49459990	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs144722464	chr6:49460004-49460005	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs368444649	chr6:49460026-49460027	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs372696964	chr6:49460032-49460033	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs554533571	chr6:49460063-49460064	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs566787635	chr6:49460090-49460091	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs533830395	chr6:49460093-49460094	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs549568758	chr6:49460145-49460146	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs1471539	chr6:49460152-49460153	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs377241945	chr6:49460168-49460169	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs576936215	chr6:49460199-49460200	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs1471538	chr6:49460268-49460269	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs556255367	chr6:49460281-49460282	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs183888285	chr6:49460457-49460458	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs11554555	chr6:49460460-49460461	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs148692494	chr6:49460472-49460473	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs532059725	chr6:49460552-49460553	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs551649425	chr6:49460588-49460589	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs541896969	chr6:49460634-49460635	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs559869048	chr6:49460723-49460724	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs528813777	chr6:49460726-49460727	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs540535000	chr6:49460728-49460729	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs189396607	chr6:49460742-49460743	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs199576942	chr6:49460766-49460767	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs11335563	chr6:49460770-49460771	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs568958575	chr6:49460771-49460772	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs3209645	chr6:49460772-49460773	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs200487614	chr6:49460773-49460774	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs13217564	chr6:49460785-49460786	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs532550151	chr6:49460873-49460874	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2127760	chr6:49460895-49460896	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs139049621	chr6:49460909-49460910	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs556302749	chr6:49460910-49460911	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs368421929	chr6:49460911-49460912	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs530131215	chr6:49460956-49460957	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs570957607	chr6:49460992-49460993	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs141398825	chr6:49461050-49461051	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs533548212	chr6:49461053-49461054	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192402074	chr6:49461094-49461095	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372470290	chr6:49461206-49461207	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs185635714	chr6:49461213-49461214	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs150432142	chr6:49461231-49461232	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs534116791	chr6:49461236-49461237	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs112465169	chr6:49461263-49461264	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs570636909	chr6:49461334-49461335	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs554070624	chr6:49461335-49461336	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs563944100	chr6:49461337-49461338	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs561940202	chr6:49461340-49461341	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs190055697	chr6:49461343-49461344	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
Melanoma	18172304	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
Hodgkin''s lymphoma	17606441	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
Ovarian cancer	21720365	CNVD
Osteosarcoma	21197465	CNVD
Gastric cancer	24379144	CNVD
Neuroblastoma	18923191	CNVD
abnormal development	18461090	CNVD
Breast cancer	17603634	CNVD
Breast cancer	21364760	CNVD
Follicular lymphoma	16790693	CNVD
Osteosarcoma	19286668	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	16608533	CNVD
Olfactory neuroblastoma	18408657	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
Bladder cancer	21909424	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:159 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49431800-49461200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:49431800-49462000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:49432000-49462000	Weak transcription	Brain Angular Gyrus	brain
4	chr6:49432000-49463000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:49432200-49461600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:49432200-49462400	Weak transcription	Fetal Lung	lung
7	chr6:49432200-49462800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:49432200-49463800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:49432600-49460600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:49432600-49472000	Weak transcription	NHEK	skin
12	chr6:49433200-49461200	Weak transcription	NHDF-Ad	bronchial
13	chr6:49440400-49460000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
15	chr6:49441000-49464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:49441200-49461800	Weak transcription	A549	lung
17	chr6:49446000-49460200	Weak transcription	Stomach Mucosa	stomach
18	chr6:49446800-49461800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:49447800-49460400	Weak transcription	Right Ventricle	heart
20	chr6:49448400-49464600	Weak transcription	Gastric	stomach
21	chr6:49448600-49460400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:49449400-49460200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:49449800-49463000	Weak transcription	Lung	lung
24	chr6:49449800-49465000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:49450400-49461400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:49450400-49464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:49450600-49462600	Weak transcription	Thymus	Thymus
28	chr6:49450600-49464000	Weak transcription	Spleen	Spleen
29	chr6:49451000-49461800	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
31	chr6:49451600-49464000	Weak transcription	Fetal Stomach	stomach
32	chr6:49453800-49462000	Strong transcription	Dnd41	blood
33	chr6:49454000-49465200	Weak transcription	Fetal Brain Male	brain
34	chr6:49454800-49463400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:49455000-49462200	Weak transcription	Psoas Muscle	Psoas
36	chr6:49455200-49460000	Weak transcription	Osteobl	bone
37	chr6:49455200-49460400	Strong transcription	Primary T cells from cord blood	blood
38	chr6:49455200-49461600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:49455200-49463600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:49455400-49461400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:49455600-49460600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:49455600-49461800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:49455600-49461800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:49455600-49461800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:49455600-49462200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:49455800-49462000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:49456000-49461600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:49456200-49460600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:49456200-49461400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:49456200-49461400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links