Variant report

Variant	rs1358083
Chromosome Location	chr7:146094278-146094279
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10224007	0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs10225925	1.00[CHB][hapmap]
rs10227977	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10231549	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10231672	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10235457	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10237250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs10242387	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10245855	1.00[CHB][hapmap]
rs10246857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs10248899	1.00[CHB][hapmap]
rs10249269	1.00[CHB][hapmap]
rs10256837	1.00[ASN][1000 genomes]
rs10258224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260495	1.00[CHB][hapmap]
rs10269297	1.00[CHB][hapmap]
rs10273261	1.00[ASN][1000 genomes]
rs10275558	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10280011	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10487935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11971943	1.00[GIH][hapmap]
rs11977983	1.00[CHB][hapmap]
rs11978155	1.00[CHB][hapmap]
rs11980503	1.00[CHB][hapmap]
rs12113340	1.00[CHB][hapmap]
rs1358079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1358082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403008	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs1403009	1.00[ASN][1000 genomes]
rs1403010	1.00[ASN][1000 genomes]
rs1526162	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1639456	1.00[CHB][hapmap]
rs1639478	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639479	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639485	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639487	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs17170042	1.00[CHB][hapmap]
rs17170050	1.00[CHB][hapmap]
rs17170051	1.00[CHB][hapmap]
rs17170055	1.00[CHB][hapmap]
rs17170058	1.00[CHB][hapmap]
rs17170073	1.00[CHB][hapmap]
rs17170092	0.85[CEU][hapmap]
rs1718073	1.00[ASN][1000 genomes]
rs1718074	1.00[ASN][1000 genomes]
rs1718075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718078	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718080	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718081	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1718082	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724526	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1724527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1724529	1.00[ASN][1000 genomes]
rs1724531	1.00[ASN][1000 genomes]
rs1724535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1724536	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860683	1.00[CHB][hapmap]
rs2058377	0.96[YRI][hapmap]
rs2109695	0.96[YRI][hapmap]
rs2535752	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687551	1.00[ASN][1000 genomes]
rs34086340	0.80[AFR][1000 genomes]
rs60409856	1.00[ASN][1000 genomes]
rs73738703	1.00[ASN][1000 genomes]
rs73738715	1.00[ASN][1000 genomes]
rs73738756	1.00[ASN][1000 genomes]
rs7778058	1.00[CHB][hapmap]

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	nsv889384	chr7:145541783-146239545	Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1020950	chr7:145683419-146264304	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv889387	chr7:145903862-146239545	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv533345	chr7:145934546-146134958	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv889389	chr7:145998111-146121539	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv917027	chr7:146069317-146194011	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1024679	chr7:146091479-146248268	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1358083	CNTNAP2	cis	cerebellum	SCAN
rs1358083	TPK1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:146089000-146109400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:146094200-146094600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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