Variant report

Variant	rs1352117
Chromosome Location	chr8:50850385-50850386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10086004	0.80[EUR][1000 genomes]
rs10089399	0.80[EUR][1000 genomes]
rs10090657	0.80[EUR][1000 genomes]
rs10092384	0.80[EUR][1000 genomes]
rs10504092	0.80[EUR][1000 genomes]
rs1074385	0.81[EUR][1000 genomes]
rs11785147	0.80[EUR][1000 genomes]
rs12542041	0.80[EUR][1000 genomes]
rs13251355	0.81[EUR][1000 genomes]
rs13267366	0.91[CEU][hapmap]
rs1352112	0.80[EUR][1000 genomes]
rs1385311	0.80[CEU][hapmap]
rs1385974	0.80[EUR][1000 genomes]
rs1385975	0.80[EUR][1000 genomes]
rs1486241	0.80[EUR][1000 genomes]
rs1486242	0.80[EUR][1000 genomes]
rs1486243	0.80[EUR][1000 genomes]
rs1486251	0.80[EUR][1000 genomes]
rs1486252	0.80[EUR][1000 genomes]
rs1486258	0.85[TSI][hapmap]
rs1552372	0.80[EUR][1000 genomes]
rs1580468	0.81[EUR][1000 genomes]
rs167629	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs167630	0.80[CEU][hapmap]
rs16914070	1.00[ASN][1000 genomes]
rs17674389	0.81[CEU][hapmap]
rs17674783	0.80[EUR][1000 genomes]
rs17747294	0.80[EUR][1000 genomes]
rs17747567	0.80[EUR][1000 genomes]
rs17747896	0.80[EUR][1000 genomes]
rs17747929	0.80[EUR][1000 genomes]
rs182646	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs2129162	0.81[EUR][1000 genomes]
rs2129165	0.81[EUR][1000 genomes]
rs2170953	0.88[TSI][hapmap]
rs2200494	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs223081	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2385544	0.80[EUR][1000 genomes]
rs2385545	0.80[EUR][1000 genomes]
rs2385546	0.81[EUR][1000 genomes]
rs2385547	0.81[EUR][1000 genomes]
rs2385548	0.81[EUR][1000 genomes]
rs2385554	0.88[TSI][hapmap]
rs2449957	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2449958	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs2450285	0.91[EUR][1000 genomes]
rs2450288	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs2450291	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2628417	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs2630550	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs318860	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs318862	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs318864	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs318870	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs318871	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs318872	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs318873	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs318875	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs318877	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs318884	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs318885	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs318888	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs318890	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs318893	0.80[CEU][hapmap]
rs318894	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs318902	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs318903	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs318905	0.80[CEU][hapmap]
rs318906	0.80[CEU][hapmap]
rs318908	0.80[CEU][hapmap]
rs318910	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs318911	0.80[CEU][hapmap]
rs318912	0.80[CEU][hapmap]
rs365318	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs366526	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs380279	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs384406	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs391798	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs402156	0.91[EUR][1000 genomes]
rs406337	0.93[EUR][1000 genomes]
rs415276	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs436688	0.92[EUR][1000 genomes]
rs4377975	0.81[EUR][1000 genomes]
rs4383988	0.80[EUR][1000 genomes]
rs4584153	0.80[EUR][1000 genomes]
rs55920504	0.81[EUR][1000 genomes]
rs57585353	0.80[EUR][1000 genomes]
rs58597929	0.81[EUR][1000 genomes]
rs58740018	1.00[ASN][1000 genomes]
rs60061614	0.80[EUR][1000 genomes]
rs6472722	0.90[CEU][hapmap]
rs7008924	0.80[EUR][1000 genomes]
rs7013903	0.80[EUR][1000 genomes]
rs72638307	0.80[EUR][1000 genomes]
rs72638311	0.80[EUR][1000 genomes]
rs72638312	0.80[EUR][1000 genomes]
rs72638332	0.80[EUR][1000 genomes]
rs72638338	0.81[EUR][1000 genomes]
rs7825552	0.80[EUR][1000 genomes]
rs9298228	0.80[EUR][1000 genomes]
rs9298229	0.80[EUR][1000 genomes]
rs964011	0.80[EUR][1000 genomes]
rs967109	0.93[EUR][1000 genomes]
rs967110	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs967116	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs9886451	0.80[EUR][1000 genomes]
rs993552	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1352117	SNTG1	cis	cerebellum	SCAN
rs1352117	SNTG1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50838600-50854400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:50838800-50853200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr8:50842200-50850400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:50848800-50857800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr8:50850200-50850400	Enhancers	HUES64 Cell Line	embryonic stem cell

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