Variant report

Variant	rs1397880
Chromosome Location	chr3:24069025-24069026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1133926	0.97[ASN][1000 genomes]
rs1136155	0.87[ASN][1000 genomes]
rs11706297	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710647	0.93[ASN][1000 genomes]
rs11710679	0.81[ASN][1000 genomes]
rs11711073	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711380	0.87[ASN][1000 genomes]
rs11713246	0.97[ASN][1000 genomes]
rs11718625	0.87[ASN][1000 genomes]
rs12497944	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13314607	0.97[ASN][1000 genomes]
rs13318927	0.87[ASN][1000 genomes]
rs13325754	0.97[ASN][1000 genomes]
rs1567581	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014081	0.82[ASN][1000 genomes]
rs17787211	0.81[ASN][1000 genomes]
rs2361013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28522849	0.93[ASN][1000 genomes]
rs28623591	0.87[ASN][1000 genomes]
rs34476593	0.87[ASN][1000 genomes]
rs35711415	0.97[ASN][1000 genomes]
rs35886023	0.93[ASN][1000 genomes]
rs4131864	0.97[ASN][1000 genomes]
rs60699428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61294694	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61645368	0.81[ASN][1000 genomes]
rs62253361	0.97[ASN][1000 genomes]
rs62253380	0.97[ASN][1000 genomes]
rs62253382	0.97[ASN][1000 genomes]
rs62253383	0.88[ASN][1000 genomes]
rs62253387	0.90[ASN][1000 genomes]
rs6550809	0.82[ASN][1000 genomes]
rs6787216	0.87[ASN][1000 genomes]
rs6789983	0.87[ASN][1000 genomes]
rs73825116	0.81[ASN][1000 genomes]
rs73825124	0.81[ASN][1000 genomes]
rs73825170	0.87[ASN][1000 genomes]
rs73825178	0.87[ASN][1000 genomes]
rs73825181	0.97[ASN][1000 genomes]
rs7629325	0.97[ASN][1000 genomes]
rs8933	0.87[ASN][1000 genomes]
rs938078	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815334	0.87[ASN][1000 genomes]
rs9834166	0.97[ASN][1000 genomes]
rs9836860	0.87[ASN][1000 genomes]
rs9836970	0.87[ASN][1000 genomes]
rs9838694	0.97[ASN][1000 genomes]
rs9850255	0.87[ASN][1000 genomes]
rs9856727	0.90[ASN][1000 genomes]
rs9857442	0.87[ASN][1000 genomes]
rs9863605	0.90[ASN][1000 genomes]
rs9863674	0.97[ASN][1000 genomes]
rs9875213	0.97[ASN][1000 genomes]
rs9876561	0.87[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1397880	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs1397880	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24061000-24069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:24065000-24070000	Weak transcription	Ovary	ovary
3	chr3:24069000-24069200	Enhancers	Fetal Brain Male	brain
4	chr3:24069000-24070600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:24069000-24070600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:24069000-24070800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:24069000-24070800	Enhancers	Cortex derived primary cultured neurospheres	brain

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