Variant report

Variant	rs134547
Chromosome Location	chr22:28801009-28801010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28799731..28802311-chr22:28804363..28806927,2	MCF-7	breast:

Extended variants
information (count: 148 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10084639	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10212083	0.91[CEU][hapmap]
rs10222318	0.82[AMR][1000 genomes];0.94[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	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12165893	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12165913	0.82[AFR][1000 genomes]
rs12166245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12166475	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]
rs12167122	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12167434	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12167532	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12167614	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12167735	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs12168031	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12168765	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12169071	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12169120	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12169232	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12169460	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12169880	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[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];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs134194	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap]
rs134197	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs134488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[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];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[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];0.93[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.85[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];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs134528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16986177	1.00[CHB][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	0.83[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];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]
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]
rs17487463	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2144922	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]
rs2881496	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28818228	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35438111	1.00[ASN][1000 genomes]
rs55738739	0.82[AMR][1000 genomes]
rs5752754	0.83[EUR][1000 genomes]
rs5762574	1.00[ASN][1000 genomes]
rs58049055	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58542867	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60042154	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6005807	0.91[CEU][hapmap]
rs6005809	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60065194	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60248971	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60693420	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6519751	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6519752	1.00[ASN][1000 genomes]
rs6519753	0.82[AMR][1000 genomes]
rs6519758	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7285440	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7288792	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7289534	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291268	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs7293232	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73430118	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430168	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73430179	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73430189	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73432205	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73439811	0.82[AMR][1000 genomes]
rs738200	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs738627	0.82[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	0.81[AFR][1000 genomes]
rs8136767	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8136905	0.81[AFR][1000 genomes]
rs8136995	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8137808	0.82[AMR][1000 genomes]
rs8142681	0.88[AFR][1000 genomes]
rs9306457	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs9620778	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9620779	0.91[CEU][hapmap]
rs9620797	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs9620799	0.82[AMR][1000 genomes]
rs9620803	0.82[AMR][1000 genomes]
rs9620804	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs9620808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9620809	0.82[AFR][1000 genomes]
rs9620810	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9620811	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[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];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9625477	0.91[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs9625478	0.83[CEU][hapmap]
rs9625481	0.82[AMR][1000 genomes]
rs9625484	0.82[AMR][1000 genomes]
rs9625498	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625509	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625512	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9625513	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9625514	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625516	0.82[AFR][1000 genomes]
rs9625518	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9625520	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625521	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625522	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625523	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625524	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs134547	SEZ6L	cis	cerebellum	SCAN
rs134547	TTC28	cis	lymphoblastoid	seeQTL
rs134547	GAL3ST1	cis	cerebellum	SCAN
rs134547	TXNDC2	trans	cerebellum	SCAN
rs134547	C22orf15	cis	cerebellum	SCAN
rs134547	TMEM211	cis	cerebellum	SCAN
rs134547	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:28792800-28805200	Weak transcription	Fetal Intestine Large	intestine
3	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
4	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
6	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
7	chr22:28793400-28806200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:28794200-28806000	Weak transcription	NHDF-Ad	bronchial
9	chr22:28794600-28804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr22:28794600-28804800	Weak transcription	Fetal Stomach	stomach
11	chr22:28794600-28806000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:28794600-28806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr22:28795000-28803400	Weak transcription	Brain Anterior Caudate	brain
14	chr22:28795200-28803200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr22:28796600-28802200	Weak transcription	Fetal Brain Female	brain
16	chr22:28798400-28802600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:28798400-28809800	Weak transcription	Fetal Lung	lung
18	chr22:28798600-28803400	Weak transcription	Brain Hippocampus Middle	brain
19	chr22:28798800-28821200	Weak transcription	Dnd41	blood
20	chr22:28799600-28804600	Weak transcription	Psoas Muscle	Psoas
21	chr22:28800800-28802200	Weak transcription	Fetal Brain Male	brain
22	chr22:28801000-28804800	Weak transcription	Colon Smooth Muscle	Colon
23	chr22:28801000-28810000	Weak transcription	Fetal Kidney	kidney

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