Variant report

Variant	rs2963826
Chromosome Location	chr5:59096923-59096924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:72953949..72954648-chr5:59096665..59097397,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1008709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1027747	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10514857	0.87[MEX][hapmap]
rs10940649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1120533	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11951422	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11956684	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12187752	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs12523468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13155799	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs13168347	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13173398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1504982	0.87[EUR][1000 genomes]
rs168883	0.87[CHB][hapmap]
rs17310599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17311853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17311925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17371174	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17830249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2067024	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2898247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2938780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938783	0.82[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.93[ASN][1000 genomes]
rs2938786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2963817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2963818	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2963821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2963822	0.93[ASN][1000 genomes]
rs2963825	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298063	0.89[TSI][hapmap]
rs298084	0.89[TSI][hapmap]
rs298091	0.91[TSI][hapmap]
rs3111173	0.95[ASN][1000 genomes]
rs34380238	0.93[ASN][1000 genomes]
rs36143327	0.84[EUR][1000 genomes]
rs4577665	0.88[EUR][1000 genomes]
rs4699942	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4700342	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56312915	1.00[ASN][1000 genomes]
rs60204066	0.80[ASN][1000 genomes]
rs6450530	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs6860907	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs6885294	0.93[ASN][1000 genomes]
rs6889294	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs72751266	1.00[ASN][1000 genomes]
rs72751270	0.98[ASN][1000 genomes]
rs72751273	0.93[ASN][1000 genomes]
rs72751280	0.95[ASN][1000 genomes]
rs72751283	0.95[ASN][1000 genomes]
rs72751285	0.93[ASN][1000 genomes]
rs72751288	0.93[ASN][1000 genomes]
rs72751293	0.84[ASN][1000 genomes]
rs72751296	0.80[ASN][1000 genomes]
rs72751298	0.80[ASN][1000 genomes]
rs7703963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7718249	0.85[ASN][1000 genomes]
rs7730821	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs877745	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs981230	0.87[MEX][hapmap]
rs986400	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[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	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59087400-59106000	Weak transcription	Aorta	Aorta
2	chr5:59095200-59097200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:59095200-59097400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr5:59095400-59097000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:59095400-59097800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:59095600-59097400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:59096000-59097200	Weak transcription	Fetal Lung	lung
8	chr5:59096000-59098000	Enhancers	Hela-S3	cervix
9	chr5:59096000-59101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:59096200-59097000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:59096400-59097000	Enhancers	A549	lung
12	chr5:59096400-59106000	Weak transcription	Fetal Brain Male	brain
13	chr5:59096600-59097400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:59096800-59097800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:59096800-59101800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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