Variant report

Variant	rs2144922
Chromosome Location	chr22:28923317-28923318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10084639	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10222318	0.91[EUR][1000 genomes]
rs10483151	0.83[CEU][hapmap]
rs12165715	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12165893	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12165913	0.85[AFR][1000 genomes]
rs12166245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12166475	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12167122	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12167434	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12167532	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12167614	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12168031	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12168765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12169071	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12169120	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12169232	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12169262	1.00[CEU][hapmap]
rs12169460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12169880	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12171099	0.87[AFR][1000 genomes]
rs134488	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs134506	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs134514	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs134524	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs134547	1.00[CEU][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1474961	0.83[CEU][hapmap];0.88[MEX][hapmap]
rs16986398	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16986509	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs17413461	0.83[CEU][hapmap]
rs17507066	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180459	0.86[ASN][1000 genomes]
rs2346866	0.86[ASN][1000 genomes]
rs2881496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28818228	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs5752754	0.88[EUR][1000 genomes]
rs5752756	0.92[ASN][1000 genomes]
rs5762667	0.94[ASN][1000 genomes]
rs5762706	0.86[ASN][1000 genomes]
rs58049055	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs58542867	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60042154	0.81[AFR][1000 genomes]
rs6005807	0.91[CEU][hapmap];0.86[ASN][1000 genomes]
rs6005809	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60065194	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60248971	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs60693420	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6519758	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs695289	0.89[ASN][1000 genomes]
rs695294	0.86[ASN][1000 genomes]
rs695305	0.89[ASN][1000 genomes]
rs695344	0.89[ASN][1000 genomes]
rs695346	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs695365	0.86[ASN][1000 genomes]
rs695442	0.89[ASN][1000 genomes]
rs695529	0.81[ASN][1000 genomes]
rs695555	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs695571	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs695575	0.86[ASN][1000 genomes]
rs695580	0.89[ASN][1000 genomes]
rs695609	0.89[ASN][1000 genomes]
rs695626	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs695627	0.89[ASN][1000 genomes]
rs695656	0.89[ASN][1000 genomes]
rs7288792	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7289534	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7289625	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7291268	0.91[CEU][hapmap]
rs7293232	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs73430118	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73430168	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73430179	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73430189	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73432205	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs738200	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs8135424	0.86[AFR][1000 genomes]
rs8136767	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8136905	0.86[AFR][1000 genomes]
rs8136995	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8142681	0.93[AFR][1000 genomes]
rs9306457	0.91[CEU][hapmap]
rs9608696	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9620797	0.91[CEU][hapmap]
rs9620804	0.91[CEU][hapmap]
rs9620808	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9620809	0.86[AFR][1000 genomes]
rs9620810	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9620811	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625467	0.91[CEU][hapmap]
rs9625475	0.91[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap]
rs9625477	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs9625478	0.83[CEU][hapmap]
rs9625498	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625509	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9625512	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625513	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625514	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625516	0.86[AFR][1000 genomes]
rs9625518	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625520	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625521	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625522	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9625523	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625524	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625534	0.83[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	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2144922	CABP7	cis	cerebellum	SCAN
rs2144922	C22orf15	cis	cerebellum	SCAN
rs2144922	TFIP11	cis	cerebellum	SCAN
rs2144922	TTC28	cis	lymphoblastoid	seeQTL
rs2144922	GAL3ST1	cis	cerebellum	SCAN
rs2144922	CHEK2	cis	lymphoblastoid	seeQTL
rs2144922	SEZ6L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28913400-28923800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:28916000-28924400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr22:28916600-28935800	Weak transcription	Fetal Lung	lung
4	chr22:28916600-28937200	Weak transcription	HepG2	liver
5	chr22:28917600-28943200	Weak transcription	Left Ventricle	heart
6	chr22:28918000-28924800	Weak transcription	Fetal Muscle Leg	muscle
7	chr22:28918000-28926000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr22:28918000-28928400	Weak transcription	Ovary	ovary
9	chr22:28919600-28925400	Weak transcription	Fetal Stomach	stomach
10	chr22:28920800-28925200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr22:28923200-28924000	Enhancers	Pancreas	Pancrea

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