Variant report

Variant	rs11161912
Chromosome Location	chr1:76405162-76405163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873797	1.00[JPT][hapmap]
rs10873804	0.81[GIH][hapmap]
rs11161848	1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs1146631	1.00[JPT][hapmap]
rs1146634	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1146635	0.84[GIH][hapmap]
rs1146636	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1146644	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12043473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12130832	1.00[JPT][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12164500	0.83[CEU][hapmap]
rs12410373	0.81[GIH][hapmap]
rs1463812	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1498311	1.00[JPT][hapmap]
rs1628063	1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs1689273	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17647178	1.00[JPT][hapmap]
rs1770889	1.00[JPT][hapmap]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1856791	1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs2083175	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795251	0.81[GIH][hapmap]
rs5745323	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs6593520	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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[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]
rs6656501	1.00[JPT][hapmap]
rs721204	1.00[JPT][hapmap]
rs7543749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552289	0.84[GIH][hapmap]
rs7555203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879268	1.00[JPT][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11161912	RABGGTB	cis	cerebellum	SCAN
rs11161912	SNORD45B	cis	cerebellum	SCAN
rs11161912	MSH4	cis	parietal	SCAN
rs11161912	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs11161912	MSH4	cis	cerebellum	SCAN
rs11161912	ACADM	cis	cerebellum	SCAN
rs11161912	MSH4	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76402800-76420000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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