Variant report

Variant	rs3138107
Chromosome Location	chr1:158263766-158263767
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12565919	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1321646	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16840031	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs16840041	0.84[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs16840093	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16840096	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269714	0.84[JPT][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs2269715	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2269716	0.83[ASN][1000 genomes]
rs2269717	0.83[ASN][1000 genomes]
rs3136533	0.84[JPT][hapmap];0.86[MKK][hapmap];0.81[ASN][1000 genomes]
rs3181031	0.83[ASN][1000 genomes]
rs3181082	0.84[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41516545	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61818724	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61818725	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61818727	0.86[ASN][1000 genomes]
rs61818738	0.82[ASN][1000 genomes]
rs6660005	0.83[ASN][1000 genomes]
rs7530662	0.85[LWK][hapmap]
rs962879	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv831692	chr1:158223459-158392016	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3138107	MTX1	cis	parietal	SCAN
rs3138107	FDPS	cis	cerebellum	SCAN
rs3138107	S100A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158257200-158264000	Enhancers	Dnd41	blood
2	chr1:158261600-158263800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
3	chr1:158261800-158263800	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr1:158261800-158264200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
5	chr1:158263600-158263800	Enhancers	Thymus	Thymus

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