Variant report

Variant	rs12901243
Chromosome Location	chr15:75374233-75374234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12148488	0.93[YRI][hapmap]
rs12185077	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12185078	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12185102	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12324912	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591119	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593542	0.81[LWK][hapmap]
rs12708514	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12917120	0.91[CHB][hapmap];0.83[CHD][hapmap];0.94[LWK][hapmap];0.89[YRI][hapmap]
rs13056	0.88[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs1867146	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867150	0.88[AFR][1000 genomes]
rs2083731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120019	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2120020	0.88[AFR][1000 genomes]
rs2289582	0.85[CEU][hapmap]
rs2304899	0.83[YRI][hapmap]
rs2304903	0.88[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.87[AFR][1000 genomes]
rs2415253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415254	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2415255	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34237279	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34655806	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34713999	0.82[AFR][1000 genomes]
rs34835684	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34913788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35577967	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35736167	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35911108	0.87[AFR][1000 genomes]
rs3812944	0.83[YRI][hapmap]
rs3850093	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap]
rs5020842	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes]
rs60425110	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6495135	0.87[LWK][hapmap]
rs6495147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67324798	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs67538199	0.87[ASN][1000 genomes]
rs67544533	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163390	0.85[LWK][hapmap]
rs7163636	0.83[YRI][hapmap]
rs7167285	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7174129	0.87[LWK][hapmap]
rs7175720	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342591	0.87[LWK][hapmap]
rs7342601	0.85[LWK][hapmap]
rs8028632	0.88[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs8030089	0.83[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs8033837	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033925	0.82[AFR][1000 genomes]
rs8036197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039755	0.82[YRI][hapmap]
rs8040169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042409	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042558	0.87[LWK][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12901243	GLCE	cis	cerebellum	SCAN
rs12901243	ULK3	cis	parietal	SCAN
rs12901243	CYP1A1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75374000-75374600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:75374000-75375400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr15:75374200-75374800	Enhancers	Monocytes-CD14+_RO01746	blood

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