Variant report

Variant	rs2579903
Chromosome Location	chr8:35442313-35442314
allele	C/T
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	0.82[EUR][1000 genomes]
rs13266983	0.82[EUR][1000 genomes]
rs1439155	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439160	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	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2067700	1.00[EUR][1000 genomes]
rs2099682	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2579901	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2579904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589334	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589335	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589336	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589339	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589343	1.00[EUR][1000 genomes]
rs2589346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589351	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589352	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589746	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589747	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589755	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589761	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2589763	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918955	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918956	0.91[EUR][1000 genomes]
rs2918958	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918959	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2918964	0.85[EUR][1000 genomes]
rs2918965	0.85[EUR][1000 genomes]
rs2918973	0.88[EUR][1000 genomes]
rs2918976	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2958249	0.94[EUR][1000 genomes]
rs2958251	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958252	0.91[EUR][1000 genomes]
rs2958253	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	0.94[EUR][1000 genomes]
rs2978568	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2978569	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	0.82[EUR][1000 genomes]
rs2978583	0.81[EUR][1000 genomes]
rs2978585	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4481588	0.82[EUR][1000 genomes]
rs4534130	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
rs2579903	UNC5D	cis	parietal	SCAN
rs2579903	EIF4EBP1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35439400-35442400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr8:35439400-35442600	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr8:35440800-35455200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr8:35441200-35442800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr8:35441200-35442800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:35441400-35451200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:35441600-35442800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr8:35441600-35451200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:35441600-35451200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:35441600-35463600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:35441800-35444600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:35442200-35451000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:35442200-35452000	Weak transcription	H1 Cell Line	embryonic stem cell

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