Variant report

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11161912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146591	1.00[JPT][hapmap]
rs1146631	1.00[JPT][hapmap]
rs1146634	0.84[CEU][hapmap]
rs1146636	0.84[CEU][hapmap]
rs1146644	0.84[CEU][hapmap]
rs12043473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12726486	1.00[JPT][hapmap]
rs12731627	1.00[JPT][hapmap]
rs12733990	1.00[JPT][hapmap]
rs12743235	1.00[JPT][hapmap]
rs1689273	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083175	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745317	1.00[JPT][hapmap]
rs5745323	0.89[CEU][hapmap]
rs5745352	1.00[JPT][hapmap]
rs5745368	1.00[JPT][hapmap]
rs5745376	1.00[JPT][hapmap]
rs5745391	1.00[JPT][hapmap]
rs5745403	1.00[JPT][hapmap]
rs5745425	1.00[JPT][hapmap]
rs5745434	1.00[JPT][hapmap]
rs5745438	1.00[JPT][hapmap]
rs5745537	1.00[JPT][hapmap]
rs5745549	1.00[JPT][hapmap]
rs6593520	0.96[CEU][hapmap];1.00[CHB][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]
rs6593521	1.00[CEU][hapmap];1.00[CHB][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]
rs7543749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7556286	MSH4	cis	Muscle Skeletal	GTEx
rs7556286	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76402600-76403400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:76402800-76403600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:76402800-76420000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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