Variant report

Variant	rs1511536
Chromosome Location	chr3:24104259-24104260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10865794	0.80[AFR][1000 genomes]
rs10865795	0.80[AFR][1000 genomes]
rs11129133	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11925334	0.92[EUR][1000 genomes]
rs1511537	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511540	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2063480	0.85[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs2360958	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2360959	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4416337	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4561770	0.85[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4568061	0.82[JPT][hapmap]
rs4624512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60226192	0.96[EUR][1000 genomes]
rs6550840	0.88[EUR][1000 genomes]
rs6550842	0.99[EUR][1000 genomes]
rs6550844	0.92[AFR][1000 genomes]
rs6550846	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6765461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6777075	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781758	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7612158	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619618	0.80[AFR][1000 genomes]
rs7623641	0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs7634184	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7639580	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7646501	0.86[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv834639	chr3:24037113-24233925	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1004037	chr3:24064777-24143719	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1511536	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24101400-24119200	Weak transcription	Aorta	Aorta
2	chr3:24102200-24105400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:24102200-24109200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:24102200-24110400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:24102400-24106800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:24103800-24105000	Enhancers	Rectal Smooth Muscle	rectum

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