Variant report

Variant	rs951015
Chromosome Location	chr3:24053792-24053793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24047924..24049614-chr3:24052830..24055453,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10865793	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11129132	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713946	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714202	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12488759	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1397881	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1511543	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17014043	0.92[EUR][1000 genomes]
rs1949121	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2089849	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34288805	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856622	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4277632	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4297994	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4356765	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4502534	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4568061	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4858573	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858574	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6550834	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6550835	0.90[EUR][1000 genomes]
rs6550836	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795140	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7372302	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431278	0.92[EUR][1000 genomes]
rs7431344	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs954734	0.91[AMR][1000 genomes];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs951015	NR1D2	cis	Temporal Cortex	GTEx
rs951015	NR1D2	cis	lymphoblastoid	seeQTL
rs951015	NR1D2	cis	Brain Pons	GTEx
rs951015	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs951015	NR1D2	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24046400-24060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:24051800-24055000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:24051800-24055000	Enhancers	NHEK	skin
4	chr3:24053400-24053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:24053400-24054200	Weak transcription	HMEC	breast
6	chr3:24053600-24054600	Enhancers	Hela-S3	cervix
7	chr3:24053600-24065000	Weak transcription	Psoas Muscle	Psoas

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