Variant report

Variant	rs4568061
Chromosome Location	chr3:24049520-24049521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24049320..24050973-chr3:24303692..24306625,2	K562	blood:
2	chr3:24047924..24049614-chr3:24052830..24055453,2	K562	blood:
3	chr17:56707874..56710684-chr3:24048496..24050034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10865793	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129132	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133926	0.84[CHB][hapmap]
rs11711073	0.85[CHB][hapmap]
rs11713246	0.85[CHB][hapmap]
rs11713946	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714202	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488759	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497944	0.85[CHB][hapmap]
rs13325754	0.85[CHB][hapmap]
rs1397881	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511543	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17014043	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949121	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063480	0.88[JPT][hapmap]
rs2089849	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2360959	0.82[JPT][hapmap]
rs34288805	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34312629	0.87[ASN][1000 genomes]
rs3856622	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131864	0.85[CHB][hapmap]
rs4277632	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297994	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356765	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4502534	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4561770	0.88[JPT][hapmap]
rs4624512	0.82[JPT][hapmap]
rs4858573	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858574	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550835	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6550836	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6765461	0.82[JPT][hapmap]
rs6795140	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7372302	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431278	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431344	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7623641	0.86[JPT][hapmap]
rs7634184	0.88[JPT][hapmap]
rs951015	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954734	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863605	0.85[CHB][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4568061	NR1D2	cis	Temporal Cortex	GTEx
rs4568061	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs4568061	NR1D2	cis	Brain Pons	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24036000-24053400	Weak transcription	Psoas Muscle	Psoas
2	chr3:24046400-24051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:24046400-24060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:24047600-24051800	Weak transcription	NHEK	skin

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