Variant report

Variant	rs7431344
Chromosome Location	chr3:24070473-24070474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24070180..24073429-chr3:24081033..24085245,3	MCF-7	breast:
2	chr3:24069756..24072152-chr3:24077955..24079926,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10865793	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11129132	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11713946	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714202	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12488759	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1397881	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1511543	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014043	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1949121	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001209	0.81[CHB][hapmap]
rs2063480	0.82[JPT][hapmap]
rs2089849	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2360958	0.82[JPT][hapmap]
rs2360959	0.88[JPT][hapmap]
rs34288805	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3856622	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4277632	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4297994	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4356765	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4502534	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4561770	0.82[JPT][hapmap]
rs4568061	1.00[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4624512	0.89[JPT][hapmap]
rs4858573	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858574	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6550834	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6550835	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6550836	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6765461	0.89[JPT][hapmap]
rs6777075	0.81[ASN][1000 genomes]
rs6795140	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7372302	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623641	0.83[JPT][hapmap]
rs7634184	0.84[JPT][hapmap]
rs7646501	0.89[ASN][1000 genomes]
rs951015	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs954734	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7431344	NR1D2	cis	Brain Pons	GTEx
rs7431344	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs7431344	NR1D2	cis	Temporal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24069000-24070600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:24069000-24070600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:24069000-24070800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:24069000-24070800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:24070000-24070800	Enhancers	Ovary	ovary
6	chr3:24070200-24070600	Enhancers	Fetal Brain Male	brain
7	chr3:24070400-24070800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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