Variant report

Variant	rs12166475
Chromosome Location	chr22:28860167-28860168
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10084639	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10222318	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10483148	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10483150	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10483151	0.83[CEU][hapmap]
rs12165715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12165893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12165913	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12166245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12167122	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12167434	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12167532	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12167614	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12168031	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12168765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12169071	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12169120	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12169232	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12169460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12169880	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12171099	0.81[AFR][1000 genomes]
rs1297607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs134197	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs134488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs134493	1.00[ASN][1000 genomes]
rs134498	1.00[ASN][1000 genomes]
rs134501	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs134503	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs134504	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs134505	1.00[ASN][1000 genomes]
rs134506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs134508	1.00[ASN][1000 genomes]
rs134509	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs134510	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs134512	1.00[ASN][1000 genomes]
rs134513	1.00[ASN][1000 genomes]
rs134514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs134515	1.00[ASN][1000 genomes]
rs134516	1.00[ASN][1000 genomes]
rs134520	1.00[CHB][hapmap]
rs134521	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs134524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs134528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs134547	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474961	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs16986244	1.00[ASN][1000 genomes]
rs16986248	1.00[ASN][1000 genomes]
rs16986251	1.00[ASN][1000 genomes]
rs16986254	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16986257	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16986266	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16986288	1.00[ASN][1000 genomes]
rs16986308	0.82[EUR][1000 genomes]
rs16986311	1.00[ASN][1000 genomes]
rs16986314	1.00[ASN][1000 genomes]
rs16986398	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16986400	1.00[ASN][1000 genomes]
rs16986433	1.00[ASN][1000 genomes]
rs16986438	1.00[ASN][1000 genomes]
rs16986451	1.00[ASN][1000 genomes]
rs16986469	1.00[ASN][1000 genomes]
rs16986509	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs17413461	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2144922	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]
rs2881496	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28818228	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35438111	1.00[ASN][1000 genomes]
rs55738739	0.84[AMR][1000 genomes]
rs5752754	0.82[EUR][1000 genomes]
rs5762574	1.00[ASN][1000 genomes]
rs58049055	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58542867	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59262169	0.81[AMR][1000 genomes]
rs60042154	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6005807	0.91[CEU][hapmap]
rs6005809	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60065194	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60248971	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60693420	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6519751	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6519752	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6519753	0.84[AMR][1000 genomes]
rs6519758	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7288792	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7289534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291268	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs7293232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73430118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430123	0.81[AMR][1000 genomes]
rs73430168	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73430179	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73430189	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73432205	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73439811	0.84[AMR][1000 genomes]
rs738200	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs738627	0.84[AMR][1000 genomes]
rs79104	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs79107	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs79111	1.00[ASN][1000 genomes]
rs8135424	0.80[AFR][1000 genomes]
rs8136767	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8136905	0.80[AFR][1000 genomes]
rs8136995	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8137808	0.84[AMR][1000 genomes]
rs8142681	0.88[AFR][1000 genomes]
rs9306457	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs9620797	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs9620799	0.84[AMR][1000 genomes]
rs9620803	0.84[AMR][1000 genomes]
rs9620804	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs9620808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9620809	0.89[AFR][1000 genomes]
rs9620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9620811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625447	0.83[CEU][hapmap]
rs9625467	0.91[CEU][hapmap]
rs9625475	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9625477	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9625478	0.83[CEU][hapmap]
rs9625481	0.84[AMR][1000 genomes]
rs9625484	0.84[AMR][1000 genomes]
rs9625498	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625509	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625514	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625516	0.89[AFR][1000 genomes]
rs9625518	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9625520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625522	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9625523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12166475	TMEM211	cis	cerebellum	SCAN
rs12166475	CHEK2	cis	lymphoblastoid	seeQTL
rs12166475	GAL3ST1	cis	cerebellum	SCAN
rs12166475	TXNDC2	trans	cerebellum	SCAN
rs12166475	SEZ6L	cis	cerebellum	SCAN
rs12166475	TFIP11	cis	cerebellum	SCAN
rs12166475	C22orf15	cis	cerebellum	SCAN
rs12166475	TTC28	cis	lymphoblastoid	seeQTL
rs12166475	CABP7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28839800-28861200	Weak transcription	Ovary	ovary
2	chr22:28860000-28860200	Enhancers	Small Intestine	intestine
3	chr22:28860000-28860400	Enhancers	Fetal Stomach	stomach
4	chr22:28860000-28862600	Enhancers	Fetal Kidney	kidney
5	chr22:28860000-28863000	Enhancers	Fetal Intestine Large	intestine
6	chr22:28860000-28863400	Enhancers	Fetal Intestine Small	intestine

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