Variant report

Variant	rs2483139
Chromosome Location	chr1:160933065-160933066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10737178	0.83[CHB][hapmap]
rs2039223	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs2184065	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2245672	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246485	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247472	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2249409	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249933	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250174	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250193	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250304	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265239	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2265240	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265242	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2481073	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483140	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483141	0.92[CHB][hapmap]
rs2483142	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2779801	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2990694	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007155	0.84[AMR][1000 genomes]
rs4483427	0.84[ASN][1000 genomes]
rs6427563	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427571	0.82[AMR][1000 genomes]
rs6677533	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs790055	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs790056	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2483139	UHMK1	cis	cerebellum	SCAN
rs2483139	F11R	cis	lymphoblastoid	seeQTL
rs2483139	YY1AP1	cis	cerebellum	SCAN
rs2483139	SLAMF9	cis	cerebellum	SCAN
rs2483139	USF1	cis	multi-tissue	Pritchard
rs2483139	F11R	cis	parietal	SCAN
rs2483139	PAQR6	cis	cerebellum	SCAN
rs2483139	F11R	cis	cerebellum	SCAN
rs2483139	OR6K3	cis	cerebellum	SCAN
rs2483139	RIT1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160930800-160934600	Weak transcription	Ovary	ovary
2	chr1:160931000-160942000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:160931600-160933600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:160933000-160933800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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