Variant report

Variant	rs731744
Chromosome Location	chr11:56670113-56670114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10501359	0.82[ASN][1000 genomes]
rs11228836	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603620	0.92[ASN][1000 genomes]
rs11828859	0.92[JPT][hapmap]
rs12272961	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12282767	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12416998	0.92[ASN][1000 genomes]
rs12419314	0.81[ASN][1000 genomes]
rs12421316	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs12805799	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1622278	0.94[ASN][1000 genomes]
rs17640838	0.87[ASN][1000 genomes]
rs17640885	0.97[ASN][1000 genomes]
rs1783459	0.80[ASN][1000 genomes]
rs1793426	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1938751	0.81[ASN][1000 genomes]
rs1938753	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938759	0.97[ASN][1000 genomes]
rs1938760	0.97[ASN][1000 genomes]
rs2226850	0.81[ASN][1000 genomes]
rs2226851	0.81[ASN][1000 genomes]
rs4939095	0.81[ASN][1000 genomes]
rs4939097	0.81[ASN][1000 genomes]
rs56210588	0.81[ASN][1000 genomes]
rs68039795	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7111113	0.92[ASN][1000 genomes]
rs7118645	0.97[ASN][1000 genomes]
rs7119402	0.92[ASN][1000 genomes]
rs737368	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7930832	0.81[ASN][1000 genomes]
rs7940288	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943283	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947879	0.97[ASN][1000 genomes]
rs947805	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs947806	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv468577	chr11:56503728-56704042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555101	chr11:56503728-56704042	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv469960	chr11:56605222-56704042	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1045889	chr11:56624365-56737435	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv520375	chr11:56669830-56704042	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs731744	OR8J1	cis	parietal	SCAN
rs731744	OR5AP2	cis	cerebellum	SCAN
rs731744	TMX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56663800-56672400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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