Variant report

Variant	rs245166
Chromosome Location	chr5:127230393-127230394
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	chr5:127229805..127231362-chr5:127417484..127420314,2	MCF-7	breast:
2	chr5:127227228..127230654-chr5:127416663..127421842,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10491255	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13155003	0.97[ASN][1000 genomes]
rs13166824	0.97[ASN][1000 genomes]
rs13187008	0.97[ASN][1000 genomes]
rs151848	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151850	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164526	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17164533	0.96[ASN][1000 genomes]
rs17164534	0.96[ASN][1000 genomes]
rs17839667	0.96[ASN][1000 genomes]
rs245161	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245162	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245164	0.96[EUR][1000 genomes]
rs245168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245169	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245170	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836339	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs58316019	0.95[ASN][1000 genomes]
rs62375865	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734642	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7708799	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7723029	0.94[ASN][1000 genomes]
rs9327454	0.92[ASN][1000 genomes]
rs9327455	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127227400-127231000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:127228800-127234200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:127229000-127234200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:127229000-127234200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:127229000-127234200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:127229000-127234400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:127229200-127230400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:127229200-127230400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:127229200-127230400	Weak transcription	A549	lung
10	chr5:127229200-127233800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:127229200-127234000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:127229200-127234200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:127229200-127234200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:127229200-127234200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127229400-127233600	Weak transcription	Brain Angular Gyrus	brain
16	chr5:127229400-127234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:127229400-127234200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:127229400-127234200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:127229400-127234200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:127229400-127234200	Weak transcription	HMEC	breast
21	chr5:127229800-127234400	Weak transcription	NHEK	skin
22	chr5:127230200-127230800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr5:127230200-127231000	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links