Variant report

Variant	rs16986398
Chromosome Location	chr22:28815629-28815630
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10084639	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10212083	0.91[CEU][hapmap]
rs10222318	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10483148	1.00[CHB][hapmap]
rs10483150	1.00[CHB][hapmap]
rs10483151	0.83[CEU][hapmap]
rs12165715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12165893	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12165913	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12166245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12166475	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]
rs12167122	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12167434	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12167532	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12167614	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12167735	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12168031	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12168765	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12169071	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12169120	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12169232	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12169460	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12169880	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12171099	0.83[AFR][1000 genomes]
rs1297607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs134194	0.91[CEU][hapmap];1.00[MEX][hapmap]
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];0.82[EUR][1000 genomes]
rs134501	1.00[CHB][hapmap]
rs134503	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs134504	1.00[CHB][hapmap]
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];0.90[EUR][1000 genomes]
rs134509	1.00[CHB][hapmap]
rs134510	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs134514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs134520	1.00[CHB][hapmap]
rs134521	1.00[CHB][hapmap]
rs134524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs134528	1.00[CHB][hapmap]
rs134547	0.91[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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16986177	1.00[CHB][hapmap]
rs16986254	1.00[CHB][hapmap]
rs16986257	1.00[CHB][hapmap]
rs16986266	1.00[CHB][hapmap]
rs16986308	0.83[EUR][1000 genomes]
rs16986509	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs17413461	0.83[CEU][hapmap]
rs17487463	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2144922	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]
rs2881496	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28818228	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55738739	0.84[AMR][1000 genomes]
rs5752754	0.83[EUR][1000 genomes]
rs58049055	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58542867	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59262169	0.81[AMR][1000 genomes]
rs60042154	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6005807	0.91[CEU][hapmap]
rs6005809	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60065194	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60248971	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60693420	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6519751	0.84[AMR][1000 genomes]
rs6519752	0.82[AMR][1000 genomes]
rs6519753	0.84[AMR][1000 genomes]
rs6519758	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7288792	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7289534	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7291268	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs7293232	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73430118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73430123	0.81[AMR][1000 genomes]
rs73430168	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73430179	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73430189	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73432205	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[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]
rs79107	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8135424	0.82[AFR][1000 genomes]
rs8136767	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8136905	0.82[AFR][1000 genomes]
rs8136995	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8137808	0.84[AMR][1000 genomes]
rs8142681	0.89[AFR][1000 genomes]
rs9306457	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs9620778	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9620779	0.91[CEU][hapmap]
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];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9620809	0.81[AFR][1000 genomes]
rs9620810	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9620811	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625433	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs9625437	0.91[CEU][hapmap]
rs9625438	1.00[CEU][hapmap]
rs9625440	0.83[CEU][hapmap]
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];0.87[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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625509	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9625512	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625513	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625514	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625516	0.81[AFR][1000 genomes]
rs9625518	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9625520	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625521	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625522	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625523	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625524	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16986398	GAL3ST1	cis	cerebellum	SCAN
rs16986398	TTC28	cis	lymphoblastoid	seeQTL
rs16986398	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
2	chr22:28798800-28821200	Weak transcription	Dnd41	blood
3	chr22:28806800-28815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:28807400-28821200	Weak transcription	Hela-S3	cervix
5	chr22:28808400-28821400	Weak transcription	Gastric	stomach
6	chr22:28808400-28821800	Weak transcription	Psoas Muscle	Psoas
7	chr22:28810600-28816000	Weak transcription	Ovary	ovary
8	chr22:28810600-28821800	Weak transcription	Adipose Nuclei	Adipose
9	chr22:28811000-28821600	Weak transcription	Pancreas	Pancrea
10	chr22:28813400-28815800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:28813600-28816400	Enhancers	Fetal Brain Female	brain
12	chr22:28814000-28817400	Enhancers	Brain Germinal Matrix	brain
13	chr22:28814200-28818000	Enhancers	Fetal Brain Male	brain
14	chr22:28815000-28816000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr22:28815000-28816200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr22:28815200-28816200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr22:28815200-28816200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr22:28815200-28816400	Enhancers	Fetal Lung	lung
19	chr22:28815400-28816000	Weak transcription	Stomach Mucosa	stomach
20	chr22:28815400-28816200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:28815400-28816400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr22:28815400-28816400	Enhancers	Brain Hippocampus Middle	brain
23	chr22:28815600-28816000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr22:28815600-28816200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr22:28815600-28816400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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