Variant report

Variant	rs1439160
Chromosome Location	chr8:35429924-35429925
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13251122	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13266983	0.82[EUR][1000 genomes]
rs1439155	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439162	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1866484	0.88[EUR][1000 genomes]
rs1898828	1.00[EUR][1000 genomes]
rs2067700	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099682	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2579901	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2579903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579904	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589334	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589335	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589336	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589343	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2589346	1.00[EUR][1000 genomes]
rs2589351	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589352	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589746	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589747	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589755	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589761	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589762	1.00[EUR][1000 genomes]
rs2589763	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918955	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918956	0.91[EUR][1000 genomes]
rs2918958	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918959	0.91[EUR][1000 genomes]
rs2918964	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2918965	0.85[EUR][1000 genomes]
rs2918973	0.88[EUR][1000 genomes]
rs2918976	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2958249	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2958251	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958252	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2958253	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2958254	0.82[EUR][1000 genomes]
rs2958256	0.82[EUR][1000 genomes]
rs2958257	0.82[EUR][1000 genomes]
rs2978406	0.91[EUR][1000 genomes]
rs2978567	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2978568	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978569	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978573	0.91[EUR][1000 genomes]
rs2978576	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2978580	0.80[ASN][1000 genomes]
rs2978581	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2978583	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2978585	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4481588	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4534130	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[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	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520421	chr8:35155517-35479468	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv533420	chr8:35358115-36227536	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1439160	UNC5D	cis	parietal	SCAN
rs1439160	EIF4EBP1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35415000-35431000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:35419000-35430200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:35419000-35439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:35419000-35439600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr8:35423600-35432600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr8:35423800-35439400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr8:35423800-35439600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr8:35424200-35439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:35424200-35439400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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