Variant report

Variant	rs6870104
Chromosome Location	chr5:44727935-44727936
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	chr5:44722551..44725527-chr5:44726909..44728900,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10512866	0.96[EUR][1000 genomes]
rs11951477	0.87[EUR][1000 genomes]
rs11957933	0.87[EUR][1000 genomes]
rs13153376	0.87[EUR][1000 genomes]
rs13153426	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13162944	0.87[EUR][1000 genomes]
rs13163070	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13165641	0.96[EUR][1000 genomes]
rs13165992	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13166622	0.87[EUR][1000 genomes]
rs13167135	0.87[EUR][1000 genomes]
rs13167593	0.87[EUR][1000 genomes]
rs13172191	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13173899	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180428	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13183825	0.87[EUR][1000 genomes]
rs13184849	0.87[EUR][1000 genomes]
rs13185697	0.87[EUR][1000 genomes]
rs13187122	0.96[EUR][1000 genomes]
rs13187187	0.96[EUR][1000 genomes]
rs13188873	0.87[EUR][1000 genomes]
rs13188895	0.87[EUR][1000 genomes]
rs16901939	0.96[EUR][1000 genomes]
rs16901954	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16901958	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16901986	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16901987	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2330571	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34094652	0.87[EUR][1000 genomes]
rs34098474	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34133773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34172556	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34216230	0.96[EUR][1000 genomes]
rs34282174	0.96[EUR][1000 genomes]
rs34544432	0.96[EUR][1000 genomes]
rs34918593	0.96[EUR][1000 genomes]
rs34942360	0.96[EUR][1000 genomes]
rs35241613	0.87[EUR][1000 genomes]
rs35278372	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35472604	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35534193	0.96[EUR][1000 genomes]
rs35564441	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35842403	0.96[EUR][1000 genomes]
rs35850760	0.96[EUR][1000 genomes]
rs35868527	0.96[EUR][1000 genomes]
rs36163058	0.96[EUR][1000 genomes]
rs4398644	0.87[EUR][1000 genomes]
rs57288883	0.87[EUR][1000 genomes]
rs58871041	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59337658	0.87[EUR][1000 genomes]
rs60303396	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60772043	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6451785	0.87[EUR][1000 genomes]
rs6860030	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6869608	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6877331	0.87[EUR][1000 genomes]
rs6877454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881573	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6882983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6891637	0.87[EUR][1000 genomes]
rs6893211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71590654	0.87[EUR][1000 genomes]
rs7704815	0.87[EUR][1000 genomes]
rs7710153	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7735466	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7736197	0.87[EUR][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	nsv880457	chr5:44632008-44800665	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830279	chr5:44688175-44860815	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44706800-44729200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:44727200-44729400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:44727200-44729600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:44727400-44729800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:44727600-44729200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:44727600-44729200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:44727600-44729400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:44727600-44729400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links