Variant report

Variant	rs9299419
Chromosome Location	chr9:97066584-97066585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10821352	0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs10993127	0.85[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap]
rs10993144	0.82[ASN][1000 genomes]
rs10993147	0.84[ASN][1000 genomes]
rs10993151	0.85[ASN][1000 genomes]
rs12235970	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs12236219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1328305	0.89[ASN][1000 genomes]
rs16909983	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs16910109	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1752784	0.82[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs2486632	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs2769813	0.86[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs2769816	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3118766	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs4744338	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs4744345	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs639276	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs7024151	0.98[ASN][1000 genomes]
rs7024423	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7024915	1.00[ASN][1000 genomes]
rs7027606	0.85[CHB][hapmap]
rs7028040	0.85[CHB][hapmap]
rs7028530	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7042481	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409515	1.00[ASN][1000 genomes]
rs9409546	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs9409550	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9299419	ZNF484	cis	cerebellum	SCAN
rs9299419	HIATL1	cis	lymphoblastoid	seeQTL
rs9299419	HIATL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
3	chr9:97055600-97066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:97055600-97067800	Weak transcription	HepG2	liver
5	chr9:97055600-97068000	Weak transcription	Pancreas	Pancrea
6	chr9:97063600-97068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:97064200-97067600	Weak transcription	Primary T cells from cord blood	blood
8	chr9:97064200-97068000	Weak transcription	Adipose Nuclei	Adipose
9	chr9:97064800-97067400	Weak transcription	Primary B cells from cord blood	blood
10	chr9:97066200-97067000	Enhancers	Fetal Brain Male	brain
11	chr9:97066400-97067000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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