Variant report

Variant	rs1647542
Chromosome Location	chr18:11853053-11853054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:11849544-11856636	Hela-S3	cervix:	n/a	n/a
2	FOS	chr18:11852942-11853268	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr18:11849708-11855634	Hela-S3	cervix:	n/a	n/a
4	CHD1	chr18:11849434-11853974	IMR90	lung:	n/a	n/a
5	POLR2A	chr18:11849786-11855757	A549	lung:	n/a	n/a
6	POLR2A	chr18:11848810-11859649	IMR90	lung:	n/a	n/a
7	POLR2A	chr18:11849634-11853427	Hela-S3	cervix:	n/a	n/a
8	USF2	chr18:11850698-11853450	Hela-S3	cervix:	n/a	chr18:11852755-11852776 chr18:11851424-11851440
9	POLR2A	chr18:11849742-11860299	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr18:11850180-11853827	K562	blood:	n/a	n/a
11	IRF1	chr18:11852838-11853226	K562	blood:	n/a	n/a
12	POLR2A	chr18:11852861-11853647	HepG2	liver:	n/a	n/a
13	TBP	chr18:11849767-11853470	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr18:11849706-11860430	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr18:11852648-11853139	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr18:11852382..11853364-chr19:54974295..54974965,2	Hela-S3	cervix:
2	chr18:11851619..11853678-chr18:11981084..11983023,2	MCF-7	breast:
3	chr18:11848937..11853647-chr18:11979272..11982109,5	K562	blood:
4	chr18:11852816..11854453-chr18:11871185..11873560,2	MCF-7	breast:
5	chr18:11808910..11811619-chr18:11851071..11853396,2	MCF-7	breast:
6	chr18:11851217..11853122-chr18:11907362..11910210,4	MCF-7	breast:

No data

Variant related genes	Relation type
CHMP1B	TF binding region
GNAL	TF binding region
ENSG00000267165	TF binding region
ENSG00000141401	Chromatin interaction
ENSG00000141404	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000267455	Chromatin interaction
ENSG00000182909	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1249625	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1262042	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1262043	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1272340	1.00[AMR][1000 genomes]
rs1364630	1.00[AMR][1000 genomes]
rs1364634	1.00[AMR][1000 genomes]
rs1647552	1.00[AMR][1000 genomes]
rs1863121	1.00[AMR][1000 genomes]
rs6505678	1.00[AMR][1000 genomes]
rs7230614	1.00[AMR][1000 genomes]
rs7238570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8088462	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11849800-11853200	Active TSS	Colonic Mucosa	Colon
2	chr18:11849800-11853200	Active TSS	Fetal Intestine Small	intestine
3	chr18:11849800-11853200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr18:11849800-11853200	Active TSS	HSMMtube	muscle
5	chr18:11849800-11853400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:11849800-11854000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr18:11850000-11853200	Active TSS	Brain Cingulate Gyrus	brain
8	chr18:11850000-11853200	Active TSS	Ovary	ovary
9	chr18:11850000-11853200	Active TSS	Psoas Muscle	Psoas
10	chr18:11850000-11853200	Active TSS	Stomach Mucosa	stomach
11	chr18:11850000-11853800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:11850200-11853600	Active TSS	Right Ventricle	heart
13	chr18:11850200-11853800	Active TSS	Right Atrium	heart
14	chr18:11850200-11854000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:11850400-11853200	Active TSS	Fetal Thymus	thymus
16	chr18:11850600-11853200	Active TSS	Fetal Intestine Large	intestine
17	chr18:11850600-11853200	Active TSS	Fetal Stomach	stomach
18	chr18:11850600-11853200	Active TSS	NHLF	lung
19	chr18:11850600-11853600	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr18:11850600-11853800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr18:11850800-11853200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr18:11850800-11853200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr18:11850800-11853200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:11850800-11853200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:11850800-11853200	Active TSS	Fetal Kidney	kidney
26	chr18:11850800-11853400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr18:11850800-11853400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr18:11850800-11853600	Active TSS	Fetal Brain Female	brain
29	chr18:11850800-11853600	Active TSS	HMEC	breast
30	chr18:11850800-11854200	Active TSS	A549	lung
31	chr18:11851000-11853200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr18:11851200-11853400	Active TSS	Hela-S3	cervix
33	chr18:11851600-11853200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr18:11851600-11853400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr18:11851600-11853400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr18:11851800-11853400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr18:11851800-11853600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr18:11851800-11853800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr18:11851800-11853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr18:11852000-11853400	Flanking Active TSS	Liver	Liver
41	chr18:11852000-11853400	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr18:11852000-11853600	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr18:11852000-11853600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr18:11852000-11853600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr18:11852000-11853800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:11852200-11853200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:11852200-11853200	Weak transcription	Esophagus	oesophagus
48	chr18:11852200-11853200	Weak transcription	Gastric	stomach
49	chr18:11852200-11853200	Weak transcription	Pancreas	Pancrea
50	chr18:11852200-11853200	Active TSS	Skeletal Muscle Female	skeletal muscle

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