Variant report

Variant	rs646512
Chromosome Location	chr1:210453938-210453939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10489391	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863818	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119455	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119456	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12069380	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12069491	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12070628	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138216	0.82[TSI][hapmap]
rs127043	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1774107	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4844987	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4844988	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4844989	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs583148	0.86[ASN][1000 genomes]
rs587203	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs588197	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs590380	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs608791	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs628423	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs628869	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628908	0.85[TSI][hapmap]
rs645311	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs645890	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs650728	0.96[GIH][hapmap];0.82[TSI][hapmap]
rs652241	0.83[ASN][1000 genomes]
rs652256	0.83[ASN][1000 genomes]
rs661190	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs662424	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs672819	0.80[EUR][1000 genomes]
rs689248	1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs701941	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs701943	0.96[GIH][hapmap];0.82[TSI][hapmap]
rs845455	0.86[GIH][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs646512	RAPGEF5	trans	lymphoblastoid	seeQTL
rs646512	NEK2	cis	cerebellum	SCAN
rs646512	SYT14	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210453400-210454000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:210453400-210454600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:210453400-210454800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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