Variant report

Variant	rs1404296
Chromosome Location	chr3:81858474-81858475
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	chr3:81725601..81726395-chr3:81858236..81859143,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10084705	0.85[TSI][hapmap]
rs13314900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13322916	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13326721	1.00[JPT][hapmap]
rs1851922	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1973802	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315966	0.84[EUR][1000 genomes]
rs2315967	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2680271	0.85[TSI][hapmap]
rs2680275	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2680276	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2691081	0.84[EUR][1000 genomes]
rs28553548	0.82[EUR][1000 genomes]
rs28668209	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772886	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3772901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772911	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3821550	0.81[TSI][hapmap]
rs3849573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57555994	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59419728	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62267115	0.84[EUR][1000 genomes]
rs62267150	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768673	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6776410	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6785740	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6791629	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798822	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6804453	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804613	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6804697	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7623056	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7634830	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9813371	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820490	0.82[EUR][1000 genomes]
rs9824576	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs9825400	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9826933	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831301	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831360	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833851	0.81[EUR][1000 genomes]
rs9838598	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9847076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9847606	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9851559	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863136	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9863322	0.84[EUR][1000 genomes]
rs9870979	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9871474	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap]
rs9874754	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9881516	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9883954	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1404296	OGT	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81852400-81872200	Weak transcription	Left Ventricle	heart
2	chr3:81857400-81860200	Enhancers	Liver	Liver
3	chr3:81857800-81859200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:81858000-81859000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:81858200-81858800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:81858200-81859200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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