Variant report

Variant	rs12121085
Chromosome Location	chr1:154355251-154355252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10908831	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11265604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1194584	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1194585	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1194586	0.82[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs1194587	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1194592	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1194607	0.92[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap]
rs12029292	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12033720	0.90[CHD][hapmap]
rs1760794	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs17654071	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1889312	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2483712	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs4075015	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4845612	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6692515	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72696290	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72698103	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7514026	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12121085	EFNA3	cis	parietal	SCAN
rs12121085	BNIPL	cis	parietal	SCAN
rs12121085	S100A4	cis	parietal	SCAN
rs12121085	THEM4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154326800-154360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:154354800-154357600	Enhancers	Primary neutrophils fromperipheralblood	blood

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