Variant report

Variant	rs11789704
Chromosome Location	chr9:97233408-97233409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10821345	0.98[ASN][1000 genomes]
rs10821352	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10993210	0.98[ASN][1000 genomes]
rs12002028	0.99[ASN][1000 genomes]
rs12235970	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs12236219	0.90[CHB][hapmap];0.97[CHD][hapmap]
rs12236578	0.90[ASN][1000 genomes]
rs16909983	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs16910109	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1752784	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1752786	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2486632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2769813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2769816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2993948	0.87[CEU][hapmap]
rs4612412	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs4744345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55877910	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs594198	0.81[EUR][1000 genomes]
rs61628907	0.96[ASN][1000 genomes]
rs639276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042481	0.87[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap]
rs7858082	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs9409546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9409564	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409565	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9409567	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409767	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409771	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409778	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409780	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409787	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11789704	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs11789704	ZNF484	cis	cerebellum	SCAN
rs11789704	HIATL1	cis	lymphoblastoid	seeQTL
rs11789704	HIATL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97222600-97237800	Weak transcription	Stomach Mucosa	stomach
2	chr9:97233200-97234000	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:97233200-97234600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:97233400-97233800	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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