Variant report

Variant	rs7142675
Chromosome Location	chr14:25012115-25012116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10144882	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11158781	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158791	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11520369	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622189	0.82[CEU][hapmap]
rs11849539	0.92[ASN][1000 genomes]
rs12886673	0.88[GIH][hapmap]
rs12896086	0.82[CEU][hapmap]
rs12896093	0.82[CEU][hapmap]
rs1304909	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951125	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951127	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951128	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956908	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1956909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1956912	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1956913	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1956918	0.82[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs2093256	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34079088	0.91[ASN][1000 genomes]
rs3861507	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3905107	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60196546	0.87[ASN][1000 genomes]
rs62001969	0.89[ASN][1000 genomes]
rs62001970	0.80[ASN][1000 genomes]
rs62001971	0.81[EUR][1000 genomes]
rs7143951	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7155452	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8008632	0.89[ASN][1000 genomes]
rs8012655	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs987630	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045732	chr14:24914008-25019317	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7142675	CTSG	cis	multi-tissue	Pritchard
rs7142675	RPPH1	cis	cerebellum	SCAN
rs7142675	SDR39U1	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25011000-25012400	Enhancers	HMEC	breast
2	chr14:25011200-25012200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:25011200-25012200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:25011200-25012400	Enhancers	NHEK	skin
5	chr14:25011600-25012200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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