Variant report

Variant	rs7715597
Chromosome Location	chr5:40872152-40872153
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	chr5:40833772..40836669-chr5:40869821..40875738,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11744119	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs173969	0.84[GIH][hapmap]
rs178929	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1812960	0.82[AFR][1000 genomes]
rs1827364	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1910015	0.96[ASN][1000 genomes]
rs2122570	0.91[ASN][1000 genomes]
rs2271709	0.89[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2455305	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2675979	0.89[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2675981	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs324062	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs324064	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs324070	0.92[ASN][1000 genomes]
rs324071	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs324073	0.82[AFR][1000 genomes]
rs4360083	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59027389	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60480205	1.00[ASN][1000 genomes]
rs6888489	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6890698	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6895317	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73088503	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73088510	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7702096	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7725655	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	esv3444044	chr5:40860244-40888483	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7715597	NUP155	cis	parietal	SCAN
rs7715597	RPL37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40871400-40872200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:40871800-40872200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40872000-40876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links