Variant report

Variant	rs9409567
Chromosome Location	chr9:97252505-97252506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10821345	0.92[ASN][1000 genomes]
rs10821352	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10993210	0.92[ASN][1000 genomes]
rs11789704	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12002028	0.94[ASN][1000 genomes]
rs12236219	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs12236578	0.85[ASN][1000 genomes]
rs16909983	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs16910109	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1752784	0.88[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap]
rs1752786	0.84[CHB][hapmap]
rs2486632	0.88[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap]
rs2769813	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs2769816	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4612412	0.90[ASN][1000 genomes]
rs4744338	0.88[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap]
rs4744345	0.88[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs55877910	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61628907	0.91[ASN][1000 genomes]
rs639276	0.88[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs7042481	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs7858082	0.90[CHB][hapmap]
rs9409546	0.88[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs9409550	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409564	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9409565	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409767	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9409771	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409778	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9409780	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9409787	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv972423	chr9:97243765-97254596	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv614916	chr9:97245822-97273659	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv969694	chr9:97250110-97254596	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9409567	PHF2	cis	parietal	SCAN
rs9409567	ZNF484	cis	cerebellum	SCAN
rs9409567	HIATL1	cis	brain	seeQTL
rs9409567	HIATL1	cis	lymphoblastoid	seeQTL
rs9409567	SLC29A3	trans	parietal	SCAN
rs9409567	HIATL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97241800-97262800	Weak transcription	Liver	Liver

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