Variant report

Variant	rs11713378
Chromosome Location	chr3:191351574-191351575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11712348	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089779	0.92[ASN][1000 genomes]
rs13323801	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13433981	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1464649	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1464650	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464651	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365534	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2886486	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4393947	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4434185	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687226	0.93[EUR][1000 genomes]
rs4687235	0.94[EUR][1000 genomes]
rs4687237	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687239	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687251	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687252	0.92[ASN][1000 genomes]
rs57196585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57290773	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57667341	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6762390	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73204638	0.94[EUR][1000 genomes]
rs73204640	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73204641	1.00[ASN][1000 genomes]
rs73204644	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73204669	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7433470	0.94[EUR][1000 genomes]
rs7633696	0.92[ASN][1000 genomes]
rs7651123	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs9290998	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816423	0.94[EUR][1000 genomes]
rs9825110	0.83[EUR][1000 genomes]
rs9834613	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9840419	0.92[ASN][1000 genomes]
rs9844704	0.84[EUR][1000 genomes]
rs9846006	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863483	0.88[ASN][1000 genomes]
rs9875132	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879803	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882196	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1008969	chr3:191192569-191383856	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv915689	chr3:191244719-191479974	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997817	chr3:191284834-191475809	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1001082	chr3:191320636-191579587	Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv436931	chr3:191348911-191371101	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region	2 gene(s)	inside rSNPs	n/a
6	nsv437355	chr3:191348911-191371101	Enhancers ZNF genes & repeats Weak transcription Strong transcription	TF binding region	2 gene(s)	inside rSNPs	n/a
7	nsv437356	chr3:191348911-191371101	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11713378	FGF12	cis	cerebellum	SCAN
rs11713378	PPP1R2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191345400-191352600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:191345400-191361400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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