Variant report

Variant	rs2063480
Chromosome Location	chr3:24143497-24143498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:24143238-24143618	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr3:24143319-24143705	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr3:24143264-24143649	MCF10A-Er-Src	breast:	n/a	chr3:24143428-24143439
4	FOS	chr3:24143212-24143621	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:24143245-24143600	MCF10A-Er-Src	breast:	n/a	chr3:24143428-24143439
6	CEBPB	chr3:24143333-24143618	Hela-S3	cervix:	n/a	n/a
7	FOS	chr3:24143265-24143530	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr3:24143266-24143619	MCF10A-Er-Src	breast:	n/a	chr3:24143428-24143439

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24141927..24144068-chr3:24144999..24146572,2	K562	blood:
2	chr3:24142494..24143999-chr3:24147403..24150339,2	K562	blood:

Variant related genes	Relation type
NPM1P23	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11925334	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1511536	0.85[EUR][1000 genomes]
rs1511537	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1511540	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2063481	0.88[CHB][hapmap];0.80[MEX][hapmap]
rs2089848	0.88[CHB][hapmap]
rs2360958	0.84[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2360959	0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34312629	0.81[ASN][1000 genomes]
rs4416337	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4561770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568061	0.88[JPT][hapmap]
rs4624512	0.85[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs60226192	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6550840	0.88[ASN][1000 genomes]
rs6550842	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6550846	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6765461	0.84[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs6777075	0.85[EUR][1000 genomes]
rs6781758	0.88[EUR][1000 genomes]
rs7612158	0.87[EUR][1000 genomes]
rs7623641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634184	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7639580	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	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
3	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
4	nsv526740	chr3:24143273-24143497	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2063480	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24141600-24144000	Enhancers	Fetal Stomach	stomach
2	chr3:24141800-24144000	Enhancers	Fetal Lung	lung
3	chr3:24141800-24144000	Enhancers	Stomach Smooth Muscle	stomach
4	chr3:24142000-24143600	Enhancers	NHLF	lung
5	chr3:24142000-24144000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:24142000-24144400	Enhancers	NHDF-Ad	bronchial
7	chr3:24142200-24143800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:24142200-24144000	Enhancers	HSMM	muscle
9	chr3:24142400-24144000	Enhancers	Hela-S3	cervix
10	chr3:24142800-24143800	Enhancers	HSMMtube	muscle
11	chr3:24142800-24144000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:24142800-24144200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:24142800-24144400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:24143000-24143800	Enhancers	Esophagus	oesophagus
15	chr3:24143000-24143800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:24143000-24144000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:24143000-24144000	Enhancers	HMEC	breast
18	chr3:24143000-24144200	Enhancers	NHEK	skin
19	chr3:24143200-24143600	Enhancers	HepG2	liver
20	chr3:24143200-24143800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:24143200-24143800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:24143200-24143800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:24143400-24144000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:24143400-24144200	Weak transcription	Psoas Muscle	Psoas

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