Variant report

Variant	rs6550836
Chromosome Location	chr3:24062840-24062841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10865793	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11129132	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713946	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714202	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12488759	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1397881	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1511543	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17014043	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1949121	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2089849	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34288805	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3856622	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4277632	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4297994	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4356765	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4502534	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4568061	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858573	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858574	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6550834	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550835	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6777075	0.82[ASN][1000 genomes]
rs6795140	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7372302	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7431278	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431344	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646501	0.88[ASN][1000 genomes]
rs951015	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs954734	0.92[AMR][1000 genomes];0.93[EUR][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	nsv536523	chr3:24041166-24076110	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6550836	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24053600-24065000	Weak transcription	Psoas Muscle	Psoas
2	chr3:24058600-24064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:24061000-24069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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