Variant report

Variant	rs13427440
Chromosome Location	chr2:57030150-57030151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1008079	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169833	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185784	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10190939	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10193496	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10193597	0.84[EUR][1000 genomes]
rs10199089	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125650	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125651	0.89[EUR][1000 genomes]
rs11125652	0.87[EUR][1000 genomes]
rs11125660	0.92[EUR][1000 genomes]
rs11678164	0.83[EUR][1000 genomes]
rs11684449	0.95[EUR][1000 genomes]
rs11889516	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619277	0.94[EUR][1000 genomes]
rs13389774	0.87[EUR][1000 genomes]
rs13392863	0.87[EUR][1000 genomes]
rs17048326	0.83[EUR][1000 genomes]
rs17048328	0.84[EUR][1000 genomes]
rs17048412	0.91[EUR][1000 genomes]
rs17048414	0.91[EUR][1000 genomes]
rs17048423	0.91[EUR][1000 genomes]
rs17269063	0.90[EUR][1000 genomes]
rs17651589	0.96[EUR][1000 genomes]
rs1996705	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042118	0.84[EUR][1000 genomes]
rs2042119	0.83[EUR][1000 genomes]
rs2042120	0.81[EUR][1000 genomes]
rs2058993	0.83[EUR][1000 genomes]
rs2072584	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2072585	0.85[EUR][1000 genomes]
rs2112028	0.88[EUR][1000 genomes]
rs2161032	0.86[EUR][1000 genomes]
rs2216494	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2870077	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4140686	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140687	0.88[EUR][1000 genomes]
rs4544483	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671296	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55695937	0.84[EUR][1000 genomes]
rs56050106	0.88[EUR][1000 genomes]
rs59647856	0.83[EUR][1000 genomes]
rs60966744	0.83[EUR][1000 genomes]
rs62162355	0.80[EUR][1000 genomes]
rs62163429	0.89[EUR][1000 genomes]
rs6719274	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6722540	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6728372	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6730195	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6732705	0.85[EUR][1000 genomes]
rs6735845	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6742821	0.87[EUR][1000 genomes]
rs6757997	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718999	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556866	0.87[EUR][1000 genomes]
rs7557250	0.88[EUR][1000 genomes]
rs7577567	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587789	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918331	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs977375	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008859	chr2:56767452-57126026	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv535726	chr2:56767452-57126026	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv582059	chr2:56892585-57175087	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv535727	chr2:56895497-57059359	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1007347	chr2:56904928-57100439	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv582060	chr2:56941668-57137622	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1002180	chr2:57019964-57130245	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13427440	EFEMP1	cis	cerebellum	SCAN
rs13427440	TAOK3	trans	cerebellum	SCAN
rs13427440	CCDC85A	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57029400-57030200	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr2:57029400-57033200	Weak transcription	NHEK	skin
3	chr2:57029400-57034400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:57029600-57030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:57029800-57030200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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