Variant report

Variant	rs12890859
Chromosome Location	chr14:81418088-81418089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10132871	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1035145	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12147744	0.80[JPT][hapmap]
rs12586161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587883	0.86[CEU][hapmap];0.92[GIH][hapmap];0.87[EUR][1000 genomes]
rs12590236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590262	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12590277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892567	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2195101	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2284715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2284716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2284721	0.91[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs2300517	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2300520	0.95[CHD][hapmap];0.90[JPT][hapmap]
rs35298517	0.88[EUR][1000 genomes]
rs35847336	0.89[EUR][1000 genomes]
rs3742720	0.86[CEU][hapmap];0.92[GIH][hapmap];0.89[EUR][1000 genomes]
rs58078360	0.85[EUR][1000 genomes]
rs8003402	0.86[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869348	chr14:80921098-81535754	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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
2	nsv832840	chr14:81270033-81423583	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	esv2761847	chr14:81392124-81453137	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
4	nsv456346	chr14:81399692-81448382	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
5	nsv565291	chr14:81399692-81448382	Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12890859	IZUMO1	trans	parietal	SCAN
rs12890859	C14orf4	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81408800-81421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr14:81410200-81420000	Weak transcription	Dnd41	blood
3	chr14:81412600-81421000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:81415000-81421000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr14:81415600-81421000	Weak transcription	NHEK	skin
6	chr14:81415600-81421200	Weak transcription	Gastric	stomach
7	chr14:81415600-81421400	Weak transcription	Placenta	Placenta
8	chr14:81415800-81421000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:81415800-81421000	Weak transcription	Thymus	Thymus
10	chr14:81415800-81421000	Weak transcription	HMEC	breast
11	chr14:81416800-81421000	Weak transcription	Fetal Thymus	thymus

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