Variant report

Variant	esv3417112
Chromosome Location	chr19:18669858-18670380
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr19:18670199-18670348	K562	blood:	n/a	n/a
2	CUX1	chr19:18670109-18670274	GM12878	blood:	n/a	n/a
3	ESRRA	chr19:18668009-18669888	GM12878	blood:	n/a	n/a
4	MTA3	chr19:18668078-18669858	GM12878	blood:	n/a	n/a
5	MXI1	chr19:18668131-18669872	IMR90	lung:	n/a	n/a
6	POLR2A	chr19:18668085-18669872	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr19:18667793-18670191	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:18669900-18670051	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:18670066-18670161	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:18669347-18670103	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:18670369-18670405	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:18670027-18670626	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:18668217-18669878	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:18668203-18669881	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:18670243-18670262	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr19:18670374-18670522	K562	blood:	n/a	n/a
17	POLR2A	chr19:18670193-18670238	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr19:18668145-18669883	K562	blood:	n/a	n/a
19	POLR2A	chr19:18669942-18670766	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr19:18668110-18669945	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:18670052-18670087	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:18669850-18669886	GM12878	blood:	n/a	n/a
23	RCOR1	chr19:18667650-18669920	IMR90	lung:	n/a	n/a
24	TCF12	chr19:18670298-18670546	GM12878	blood:	n/a	n/a
25	ZNF384	chr19:18669026-18669923	GM12878	blood:	n/a	n/a
26	ZNF384	chr19:18669578-18669939	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18630485..18634839-chr19:18666846..18671916,7	MCF-7	breast:
2	chr19:18667740..18670829-chr19:18672165..18676171,4	K562	blood:
3	chr19:18653886..18656782-chr19:18668675..18670368,2	MCF-7	breast:
4	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
5	chr19:18643154..18644865-chr19:18669645..18671230,2	K562	blood:
6	chr19:18667424..18670168-chr19:18699281..18701481,3	MCF-7	breast:
7	chr19:18631459..18633367-chr19:18667345..18670376,4	K562	blood:
8	chr19:18653032..18656930-chr19:18667045..18670995,8	MCF-7	breast:
9	chr19:18649378..18653671-chr19:18667425..18670328,5	MCF-7	breast:
10	chr19:18666812..18670172-chr19:18680715..18684041,6	MCF-7	breast:
11	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:
12	chr19:18652388..18655450-chr19:18667016..18670630,4	K562	blood:
13	chr19:18667097..18671007-chr19:18677068..18684435,17	K562	blood:
14	chr19:18652388..18654838-chr19:18668474..18670630,2	K562	blood:
15	chr19:18630548..18633267-chr19:18667345..18670044,3	K562	blood:
16	chr19:18546792..18548978-chr19:18667741..18669982,2	K562	blood:
17	chr19:18392874..18395450-chr19:18668198..18669959,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FKBP8-1	chr19:18668585-18670453	ENSG00000268030.1

No data

Variant related genes	Relation type
KXD1	TF binding region
ENSG00000221983	chromatin interactions
ENSG00000267959	chromatin interactions
ENSG00000105700	chromatin interactions
ENSG00000269191	chromatin interactions
ENSG00000006015	chromatin interactions
ENSG00000105655	chromatin interactions
ENSG00000105701	chromatin interactions
ENSG00000268983	chromatin interactions
ENSG00000105656	chromatin interactions
ENSG00000268030	chromatin interactions

Extended variants
information (count: 16 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3803917	chr19:18669883-18669884	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs567627630	chr19:18669890-18669891	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	Overlapped CNVs	n/a
3	rs188672440	chr19:18669891-18669892	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	Overlapped CNVs	n/a
4	rs549385068	chr19:18669965-18669966	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	10 gene(s)	Overlapped CNVs	n/a
5	rs151008577	chr19:18669982-18669983	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	10 gene(s)	Overlapped CNVs	n/a
6	rs3803916	chr19:18669987-18669988	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs4808819	chr19:18670004-18670005	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
8	rs146628651	chr19:18670043-18670044	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
9	rs7343102	chr19:18670064-18670065	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs143243796	chr19:18670092-18670093	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
11	rs554814352	chr19:18670165-18670166	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
12	rs574806416	chr19:18670190-18670191	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
13	rs543025136	chr19:18670193-18670194	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
14	rs562906540	chr19:18670198-18670199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
15	rs148287381	chr19:18670345-18670346	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a
16	rs535258959	chr19:18670369-18670370	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Follicular lymphoma	20505157	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-syndromic sensorineural hearing loss	20179077	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Lung cancer	17297452	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Chordoma	18071362	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Ovarian cancer	21720365	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Basal cell lymphoma	21115979	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Breast cancer	21364760	CNVD
Mycobacterial infection	18421352	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute monocytic leukemia	16498392	CNVD
Lung cancer	18438408	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Liver carcinoma	19366792	CNVD
Colorectal cancer	19455253	CNVD
Lujan-Fryns syndrom	21521776	CNVD
Breast cancer	20409316	CNVD
Cancer	17160897	CNVD
Cancer	17440070	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	21509527	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:155 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18668200-18670000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:18668400-18670200	Active TSS	GM12878-XiMat	blood
3	chr19:18669200-18670200	Flanking Active TSS	NHEK	skin
4	chr19:18669400-18670000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:18669400-18670000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:18669400-18670000	Enhancers	Spleen	Spleen
7	chr19:18669400-18670000	Flanking Active TSS	NHLF	lung
8	chr19:18669400-18670200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:18669400-18670600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:18669400-18670600	Flanking Active TSS	Dnd41	blood
11	chr19:18669400-18672400	Weak transcription	Ovary	ovary
12	chr19:18669400-18675600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18669600-18670000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr19:18669600-18670000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr19:18669600-18670000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr19:18669600-18670000	Enhancers	Fetal Muscle Leg	muscle
17	chr19:18669600-18670000	Enhancers	Right Ventricle	heart
18	chr19:18669600-18670200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:18669600-18670400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr19:18669600-18670400	Enhancers	Brain Anterior Caudate	brain
21	chr19:18669600-18670400	Enhancers	Stomach Mucosa	stomach
22	chr19:18669600-18670600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:18669600-18670600	Enhancers	Primary B cells from cord blood	blood
24	chr19:18669600-18670600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr19:18669600-18670600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr19:18669600-18670600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:18669600-18670600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:18669600-18670600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:18669600-18670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr19:18669600-18670600	Enhancers	Brain Cingulate Gyrus	brain
31	chr19:18669600-18670800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:18669600-18670800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:18669600-18670800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr19:18669600-18671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:18669600-18672400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:18669600-18672400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:18669600-18672400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:18669600-18672400	Weak transcription	Fetal Lung	lung
39	chr19:18669600-18672400	Weak transcription	Gastric	stomach
40	chr19:18669600-18674800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:18669600-18675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:18669600-18675400	Weak transcription	Fetal Kidney	kidney
43	chr19:18669600-18677600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:18669800-18670000	Enhancers	Psoas Muscle	Psoas
45	chr19:18669800-18670000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr19:18669800-18670000	Weak transcription	A549	lung
47	chr19:18669800-18670000	Enhancers	HSMM	muscle
48	chr19:18669800-18670000	Enhancers	HUVEC	blood vessel
49	chr19:18669800-18670000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:18669800-18670200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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