Variant report

Variant	rs11856590
Chromosome Location	chr15:82580736-82580737
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1128431	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs11852244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11854157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11855145	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11856561	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs16973420	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs17354842	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2047679	0.83[YRI][hapmap]
rs2292071	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs28539162	0.80[ASN][1000 genomes]
rs28752301	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759800	0.83[YRI][hapmap]
rs3902959	0.83[YRI][hapmap]
rs3973890	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4725	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4778983	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs56394250	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57014042	0.81[ASN][1000 genomes]
rs6495644	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs67988426	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023960	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs8028284	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8032033	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs8034586	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9920827	0.87[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11856590	EFTUD1	cis	lymphoblastoid	seeQTL
rs11856590	FLJ13119	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82576200-82580800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr15:82576400-82580800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:82576400-82581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:82580400-82581800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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