Variant report

Variant	rs29959
Chromosome Location	chr5:93693070-93693071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10463187	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10491400	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11749838	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12659752	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12660022	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs160268	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160270	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160271	0.81[JPT][hapmap]
rs160272	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160273	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160275	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17082131	0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17083516	0.84[CEU][hapmap];0.83[CHB][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17083564	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17083566	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1841300	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1841301	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2010909	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2434364	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446772	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914322	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2926571	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29951	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29952	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29953	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29954	0.85[JPT][hapmap]
rs29960	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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29962	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29963	0.81[JPT][hapmap]
rs366404	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39810	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs398559	0.85[JPT][hapmap]
rs401521	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs405029	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412437	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412888	0.81[JPT][hapmap]
rs42245	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs424374	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs429519	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs431283	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442817	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs443577	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447540	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs485494	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6859083	0.83[CHB][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7705823	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706373	0.83[AMR][1000 genomes]
rs7715295	1.00[YRI][hapmap]
rs9686315	0.81[EUR][1000 genomes]
rs9763486	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9764893	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs979264	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[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	chr5:93683200-93693200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:93690000-93695600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:93690400-93693200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:93690600-93693200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:93690600-93697400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:93691800-93693200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:93691800-93693600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:93692000-93693200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:93692000-93693200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:93692600-93693200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:93692600-93693200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:93692800-93693200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr5:93692800-93695400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
16	chr5:93693000-93693200	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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