Variant report

Variant	rs602878
Chromosome Location	chr5:118125694-118125695
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118123238..118126072-chr5:118128175..118130708,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10055188	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2193964	0.80[ASN][1000 genomes]
rs371209	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs421322	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs443574	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs584789	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs602868	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs603388	0.87[AFR][1000 genomes]
rs611043	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612296	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs614505	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs625911	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs631514	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs635718	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs646134	0.81[YRI][hapmap]
rs654497	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657071	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667101	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs670035	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs682859	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv1032241	chr5:117900051-118157400	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv882768	chr5:118088385-118133786	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv882769	chr5:118088385-118154368	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv882770	chr5:118089798-118133786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv599562	chr5:118122504-118230640	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118118400-118126400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:118121800-118127000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:118122000-118127200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:118125200-118126600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:118125200-118127000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:118125200-118127600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:118125400-118126800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:118125400-118127200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:118125600-118127000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links