Variant report

Variant	rs11713246
Chromosome Location	chr3:23984229-23984230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23930082..23933040-chr3:23982116..23985334,3	K562	blood:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1133926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1136155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11706297	0.97[ASN][1000 genomes]
rs11710647	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710679	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11711073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11711380	0.90[ASN][1000 genomes]
rs11718625	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11922577	0.82[JPT][hapmap]
rs12497944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13314607	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13325754	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397880	0.97[ASN][1000 genomes]
rs1567581	1.00[ASN][1000 genomes]
rs17787211	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2063481	0.82[JPT][hapmap]
rs2089848	0.85[JPT][hapmap]
rs2361013	0.97[ASN][1000 genomes]
rs28522849	0.97[ASN][1000 genomes]
rs28623591	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34476593	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35711415	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886023	0.97[ASN][1000 genomes]
rs4131864	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4568061	0.85[CHB][hapmap]
rs60699428	0.91[ASN][1000 genomes]
rs61294694	0.97[ASN][1000 genomes]
rs61645368	0.84[ASN][1000 genomes]
rs62253361	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253380	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253382	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253383	0.91[ASN][1000 genomes]
rs62253387	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550809	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768429	0.82[JPT][hapmap]
rs6778970	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs6787216	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6789983	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800407	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs72627066	0.85[EUR][1000 genomes]
rs73825116	0.84[ASN][1000 genomes]
rs73825124	0.84[ASN][1000 genomes]
rs73825170	0.90[ASN][1000 genomes]
rs73825178	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73825181	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629325	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637968	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs8933	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs938078	0.97[ASN][1000 genomes]
rs9815334	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9834166	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836860	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838694	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850255	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9856727	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857442	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9863605	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9863674	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875213	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876561	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3341907	chr3:23984076-23984451	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11713246	NR1D2	cis	Temporal Cortex	GTEx
rs11713246	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs11713246	NR1D2	cis	Brain Pons	GTEx
rs11713246	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs11713246	NR1D2	cis	Frontal Cortex	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:23964200-23985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:23976800-23985600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:23979000-23985200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23979000-23985400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:23979200-23985600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:23980400-23985200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:23980400-23985800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:23980600-23985200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:23980600-23985200	Weak transcription	Fetal Lung	lung
11	chr3:23980800-23985200	Weak transcription	Fetal Heart	heart
12	chr3:23982200-23986000	Weak transcription	Right Atrium	heart
13	chr3:23983200-23985200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:23983400-23985200	Weak transcription	K562	blood

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