Variant report

Variant	rs4744122
Chromosome Location	chr9:94939615-94939616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10156482	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10761149	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs10761152	0.81[ASN][1000 genomes]
rs10820952	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs1152757	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1175788	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1760318	0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1960094	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3847317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3996311	0.94[CHB][hapmap]
rs471478	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs4743869	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs4744121	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6651532	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs7028854	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs710163	0.89[TSI][hapmap]
rs9409664	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4744122	CENPP	cis	parietal	SCAN
rs4744122	FBP1	cis	parietal	SCAN
rs4744122	ECM2	cis	cerebellum	SCAN
rs4744122	CENPP	cis	cerebellum	SCAN
rs4744122	ZNF484	cis	cerebellum	SCAN
rs4744122	IARS	cis	lymphoblastoid	seeQTL
rs4744122	ZNF484	cis	parietal	SCAN
rs4744122	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94937200-94943400	Weak transcription	Spleen	Spleen
2	chr9:94938000-94939800	Enhancers	Fetal Muscle Leg	muscle
3	chr9:94938000-94942600	Weak transcription	Placenta	Placenta
4	chr9:94938600-94939800	Enhancers	Fetal Muscle Trunk	muscle
5	chr9:94938600-94943800	Weak transcription	Gastric	stomach
6	chr9:94939600-94943200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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