Variant report

Variant	rs6506541
Chromosome Location	chr18:7963802-7963803
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13381990	0.92[ASW][hapmap]
rs2099932	0.83[AMR][1000 genomes]
rs28367342	0.83[AMR][1000 genomes]
rs28379285	0.83[AMR][1000 genomes]
rs28523954	1.00[AMR][1000 genomes]
rs28569201	0.83[AMR][1000 genomes]
rs28644497	1.00[AMR][1000 genomes]
rs28757770	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7239466	0.92[ASW][hapmap]
rs7239724	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7239846	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7241071	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9944589	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9945054	1.00[AMR][1000 genomes]
rs9948263	0.83[AMR][1000 genomes]
rs9949297	0.83[AMR][1000 genomes]
rs9951398	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9952921	0.83[AMR][1000 genomes]
rs9955097	0.83[AMR][1000 genomes]
rs9955973	0.83[AMR][1000 genomes]
rs9958058	0.83[AMR][1000 genomes]
rs9963467	0.83[AMR][1000 genomes]
rs9963748	1.00[AMR][1000 genomes]
rs9964734	0.92[AFR][1000 genomes]
rs9965536	1.00[AMR][1000 genomes]
rs9966712	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9967327	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv521059	chr18:7962217-7981018	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr18:7947200-7981400	Weak transcription	Fetal Stomach	stomach
3	chr18:7947400-7965600	Weak transcription	Thymus	Thymus
4	chr18:7947800-7967600	Weak transcription	Primary T cells from cord blood	blood
5	chr18:7948000-7965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr18:7948000-7967200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:7948000-7975000	Weak transcription	Pancreas	Pancrea
8	chr18:7951600-7965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:7954400-7966000	Weak transcription	Fetal Kidney	kidney
10	chr18:7955400-7965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:7956000-7965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:7956000-7966200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr18:7956000-7980800	Weak transcription	Fetal Thymus	thymus
14	chr18:7956000-7982400	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:7957600-7965200	Weak transcription	Lung	lung
16	chr18:7957600-7980600	Weak transcription	Right Ventricle	heart
17	chr18:7959000-7964200	Weak transcription	NHDF-Ad	bronchial
18	chr18:7959000-7987400	Weak transcription	Ovary	ovary
19	chr18:7959200-7982400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr18:7959800-7965400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:7959800-7967800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr18:7960000-7964200	Weak transcription	Hela-S3	cervix
23	chr18:7960800-7967000	Weak transcription	Fetal Lung	lung
24	chr18:7961200-7964800	Enhancers	A549	lung
25	chr18:7962400-7964000	Enhancers	Psoas Muscle	Psoas
26	chr18:7962600-7974000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr18:7963200-7964600	Enhancers	Brain Anterior Caudate	brain
28	chr18:7963400-7964600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr18:7963400-7964800	Enhancers	Adipose Nuclei	Adipose
30	chr18:7963600-7964000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr18:7963600-7964000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:7963600-7964000	Flanking Active TSS	Left Ventricle	heart
33	chr18:7963600-7964400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr18:7963600-7964600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:7963600-7964600	Enhancers	Osteobl	bone
36	chr18:7963600-7965000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr18:7963800-7964400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr18:7963800-7964400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr18:7963800-7964600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:7963800-7964600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:7963800-7964800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:7963800-7965000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr18:7963800-7965400	Weak transcription	Right Atrium	heart
44	chr18:7963800-7969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr18:7963800-7977400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links