Variant report

Variant	rs17021239
Chromosome Location	chr4:147132636-147132637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147131915..147134397-chr4:147145047..147146932,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250673	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10006650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10014590	0.89[ASN][1000 genomes]
rs12374409	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16998674	0.99[ASN][1000 genomes]
rs16998675	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17021186	0.81[CEU][hapmap]
rs17021241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021249	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17021264	0.85[ASN][1000 genomes]
rs17335848	0.91[YRI][hapmap]
rs17756234	0.85[CEU][hapmap]
rs17757522	0.85[CEU][hapmap]
rs17757685	0.82[CEU][hapmap]
rs17814065	0.81[CEU][hapmap]
rs1865531	0.82[CEU][hapmap]
rs28605093	0.85[ASN][1000 genomes]
rs3775498	0.81[CEU][hapmap]
rs3815967	0.81[CEU][hapmap]
rs3860098	0.90[ASN][1000 genomes]
rs4835286	0.81[CEU][hapmap]
rs55762555	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55844150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56331233	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60241278	0.95[ASN][1000 genomes]
rs60701696	0.95[ASN][1000 genomes]
rs62326849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326850	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326851	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	0.80[CEU][hapmap]
rs6816161	0.82[CEU][hapmap]
rs6816198	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6820462	0.81[CEU][hapmap]
rs6835911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839123	0.81[CEU][hapmap]
rs6843421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848943	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6849193	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6854775	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72727960	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.82[CEU][hapmap]
rs919483	0.85[CEU][hapmap]
rs9308199	0.81[CEU][hapmap]
rs9993525	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17021239	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs17021239	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17021239	RP11-6L6.2	cis	lung	GTEx
rs17021239	RP11-6L6.2	cis	Muscle Skeletal	GTEx
rs17021239	RP11-6L6.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147114000-147144800	Weak transcription	Gastric	stomach
2	chr4:147132600-147132800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:147132600-147133000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:147132600-147133000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:147132600-147133000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:147132600-147133000	Enhancers	Adipose Nuclei	Adipose
7	chr4:147132600-147133000	Enhancers	Brain Anterior Caudate	brain
8	chr4:147132600-147133000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr4:147132600-147133000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links