Variant report

Variant	rs6804453
Chromosome Location	chr3:81873269-81873270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10084705	0.85[TSI][hapmap]
rs13314900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13322916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs13326721	1.00[JPT][hapmap]
rs1404296	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851922	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1973802	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315966	0.82[EUR][1000 genomes]
rs2315967	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2680271	0.85[TSI][hapmap]
rs2680275	0.85[EUR][1000 genomes]
rs2680276	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2691081	0.82[EUR][1000 genomes]
rs28668209	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772886	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs3772901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772911	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap]
rs3821550	0.81[TSI][hapmap]
rs3849573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs57555994	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59419728	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62265681	0.81[EUR][1000 genomes]
rs62267115	0.82[EUR][1000 genomes]
rs62267150	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548778	0.81[EUR][1000 genomes]
rs6768673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6776410	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6785740	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791629	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798822	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6804613	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6804697	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7623056	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap]
rs7633528	0.81[EUR][1000 genomes]
rs7634830	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9813371	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816203	0.81[EUR][1000 genomes]
rs9820490	0.81[EUR][1000 genomes]
rs9824576	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs9825400	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9826933	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831301	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831360	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833851	0.83[EUR][1000 genomes]
rs9838598	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9847076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs9847606	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap]
rs9851559	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863136	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9863322	0.82[EUR][1000 genomes]
rs9870979	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9871474	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9874754	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[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
rs6804453	OGT	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81871000-81873800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:81871000-81874400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:81871800-81873400	Enhancers	Liver	Liver
4	chr3:81872200-81873800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:81872400-81873600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:81872400-81874000	Enhancers	Fetal Heart	heart
7	chr3:81872400-81874400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:81872600-81873400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:81872600-81873600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:81872600-81873800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:81872800-81873400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:81872800-81873400	Enhancers	Brain Germinal Matrix	brain
13	chr3:81872800-81873600	Enhancers	Fetal Lung	lung
14	chr3:81872800-81873600	Enhancers	NHDF-Ad	bronchial
15	chr3:81872800-81873800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:81872800-81873800	Flanking Active TSS	GM12878-XiMat	blood
17	chr3:81872800-81874200	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:81873000-81873400	Enhancers	Primary B cells from cord blood	blood
19	chr3:81873000-81873400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr3:81873000-81873400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:81873000-81873400	Enhancers	Fetal Kidney	kidney
22	chr3:81873000-81873600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:81873000-81874000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:81873000-81874400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr3:81873200-81873400	Enhancers	Pancreas	Pancrea
26	chr3:81873200-81873600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:81873200-81873600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr3:81873200-81873600	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:81873200-81873800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:81873200-81874000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:81873200-81874200	Enhancers	Dnd41	blood

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