Variant report

Variant	rs12905578
Chromosome Location	chr15:82581264-82581265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1045508	0.89[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs11073035	0.85[ASN][1000 genomes]
rs1174543	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs11855089	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs11855144	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11857208	0.90[ASN][1000 genomes]
rs12443224	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs13380317	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs13380319	1.00[ASW][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs1392976	0.85[ASN][1000 genomes]
rs1501371	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs1501372	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs1846910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1846911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2047678	0.91[ASN][1000 genomes]
rs2088858	0.87[ASN][1000 genomes]
rs28420834	0.86[ASN][1000 genomes]
rs28540744	0.87[ASN][1000 genomes]
rs2867579	0.88[ASN][1000 genomes]
rs3858954	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4270132	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4344697	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4778982	0.88[ASN][1000 genomes]
rs6495643	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6495647	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7164362	0.85[ASN][1000 genomes]
rs7166570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7169961	0.88[ASN][1000 genomes]
rs7173339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7173852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7176075	0.89[ASN][1000 genomes]
rs7180584	0.81[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7183805	0.89[GIH][hapmap]
rs8025353	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037224	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs8041868	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs8041924	0.88[ASN][1000 genomes]
rs8042464	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs8043108	1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs867370	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs867371	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs881308	0.88[ASN][1000 genomes]
rs9944197	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12905578	CIB2	cis	cerebellum	SCAN
rs12905578	CHRNA5	cis	parietal	SCAN
rs12905578	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs12905578	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs12905578	KIAA1024	cis	parietal	SCAN
rs12905578	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs12905578	FAM154B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82576400-82581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:82580400-82581800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:82580800-82581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:82581200-82581600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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