Variant report

Variant	rs62089513
Chromosome Location	chr18:8021921-8021922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:8008779..8010342-chr18:8020655..8023577,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10164212	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10502366	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513902	0.91[ASN][1000 genomes]
rs11081350	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081351	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081359	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12326285	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567141	0.84[ASN][1000 genomes]
rs17567847	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1942952	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1942953	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1942954	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28449906	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505217	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28615299	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34818456	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34861291	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35534506	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35608995	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62089548	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67464310	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9807748	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9807780	0.87[ASN][1000 genomes]
rs9807802	0.92[ASN][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	nsv909359	chr18:8001853-8064021	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7987600-8033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:8001400-8029200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:8001400-8029200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:8004200-8029000	Weak transcription	Gastric	stomach
5	chr18:8006600-8022200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr18:8006800-8029200	Weak transcription	Lung	lung
7	chr18:8009000-8025200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:8009000-8036200	Weak transcription	Thymus	Thymus
9	chr18:8013000-8022600	Weak transcription	Left Ventricle	heart
10	chr18:8017000-8038600	Weak transcription	NH-A	brain
11	chr18:8018200-8022600	Weak transcription	Right Ventricle	heart
12	chr18:8020400-8023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr18:8020600-8036000	Weak transcription	A549	lung
14	chr18:8020800-8038800	Weak transcription	Adipose Nuclei	Adipose
15	chr18:8021000-8024000	Weak transcription	Brain Germinal Matrix	brain
16	chr18:8021000-8029200	Weak transcription	Fetal Lung	lung
17	chr18:8021000-8029200	Weak transcription	Pancreas	Pancrea
18	chr18:8021200-8022400	Weak transcription	Colon Smooth Muscle	Colon
19	chr18:8021200-8022400	Weak transcription	Fetal Heart	heart
20	chr18:8021200-8022800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:8021200-8027000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:8021200-8052000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links