Variant report

Variant	rs29960
Chromosome Location	chr5:93694769-93694770
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:93693342..93695465-chr5:93695922..93698858,2	MCF-7	breast:
2	chr5:93687905..93690477-chr5:93693837..93696347,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10463187	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10491400	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11749838	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12659752	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12660022	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs160268	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160270	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160271	0.81[JPT][hapmap]
rs160272	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160273	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082131	0.86[CEU][hapmap];0.84[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17083516	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17083564	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17083566	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1841300	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1841301	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2010909	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2434364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2446772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914322	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2926571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29951	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29954	0.84[JPT][hapmap]
rs29959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29961	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29962	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29963	0.81[JPT][hapmap]
rs366404	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39810	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398559	0.81[JPT][hapmap]
rs401521	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405029	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412437	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412888	0.81[JPT][hapmap]
rs42245	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs424374	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429519	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431283	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs442817	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443577	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447540	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485494	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859083	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7705823	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7706373	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7715295	1.00[YRI][hapmap]
rs9686315	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9763486	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9764893	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs979264	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023191	chr5:93351646-93947928	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv537808	chr5:93351646-93947928	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2753025	chr5:93356544-93812844	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1027890	chr5:93584978-93873704	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv537809	chr5:93584978-93873704	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv882385	chr5:93589609-93697852	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv518161	chr5:93643170-93789309	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv523867	chr5:93643170-93789309	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv598950	chr5:93666346-93788579	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1023421	chr5:93679661-93911066	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93674200-93716400	Weak transcription	Hela-S3	cervix
2	chr5:93682200-93775800	Weak transcription	Ovary	ovary
3	chr5:93690000-93695600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:93690600-93697400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:93692800-93695400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
6	chr5:93693400-93696600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:93693600-93694800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:93693600-93698400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:93693800-93698600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:93694000-93695400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:93694000-93695800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:93694200-93694800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:93694200-93695000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:93694200-93698600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr5:93694400-93695800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:93694600-93696200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell

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