Variant report

Variant	rs134506
Chromosome Location	chr22:28752505-28752506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10212083	0.91[CEU][hapmap]
rs10222318	0.84[EUR][1000 genomes]
rs10483148	1.00[CHB][hapmap]
rs10483150	1.00[CHB][hapmap]
rs10483151	0.83[CEU][hapmap]
rs12165715	0.81[EUR][1000 genomes]
rs12165893	0.84[EUR][1000 genomes]
rs12166245	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12166475	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]
rs12167122	0.82[AMR][1000 genomes]
rs12167532	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12167735	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs12168765	0.84[EUR][1000 genomes]
rs12169071	0.81[EUR][1000 genomes]
rs12169120	0.81[EUR][1000 genomes]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs1297607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134501	1.00[CHB][hapmap]
rs134503	1.00[CHB][hapmap]
rs134504	1.00[CHB][hapmap]
rs134509	1.00[CHB][hapmap]
rs134510	1.00[CHB][hapmap]
rs134514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134520	1.00[CHB][hapmap]
rs134521	1.00[CHB][hapmap]
rs134524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134528	1.00[CHB][hapmap]
rs134547	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]
rs1569700	1.00[CHB][hapmap]
rs16986177	1.00[CHB][hapmap]
rs16986254	1.00[CHB][hapmap]
rs16986257	1.00[CHB][hapmap]
rs16986266	1.00[CHB][hapmap]
rs16986308	0.93[EUR][1000 genomes]
rs16986398	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]
rs16986509	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs17413461	0.83[CEU][hapmap]
rs17487463	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2144922	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2881496	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58049055	0.84[EUR][1000 genomes]
rs58542867	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6005807	0.91[CEU][hapmap]
rs6005809	0.83[EUR][1000 genomes]
rs60065194	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60248971	0.84[EUR][1000 genomes]
rs6519758	0.84[EUR][1000 genomes]
rs7285440	1.00[CHB][hapmap]
rs7288792	0.84[EUR][1000 genomes]
rs7289534	0.84[EUR][1000 genomes]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7291268	0.91[CEU][hapmap]
rs7293232	0.84[EUR][1000 genomes]
rs73430118	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73430168	0.81[EUR][1000 genomes]
rs73430179	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73432205	0.84[EUR][1000 genomes]
rs738200	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs79104	1.00[CHB][hapmap]
rs79107	1.00[CHB][hapmap]
rs8136767	0.84[EUR][1000 genomes]
rs8136995	0.84[EUR][1000 genomes]
rs9306457	0.91[CEU][hapmap]
rs9620778	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs9620779	0.91[CEU][hapmap]
rs9620797	0.91[CEU][hapmap]
rs9620804	0.91[CEU][hapmap]
rs9620808	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625433	0.83[CEU][hapmap];0.87[GIH][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];1.00[MEX][hapmap]
rs9625477	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9625478	0.83[CEU][hapmap]
rs9625498	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9625509	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9625512	0.84[EUR][1000 genomes]
rs9625513	0.84[EUR][1000 genomes]
rs9625514	0.84[EUR][1000 genomes]
rs9625518	0.84[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	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs134506	TTC28	cis	lymphoblastoid	seeQTL
rs134506	TXNDC2	trans	cerebellum	SCAN
rs134506	SEZ6L	cis	cerebellum	SCAN
rs134506	C22orf15	cis	cerebellum	SCAN
rs134506	GAL3ST1	cis	cerebellum	SCAN
rs134506	TFIP11	cis	cerebellum	SCAN
rs134506	TMEM211	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28741600-28753200	Weak transcription	Brain Germinal Matrix	brain
2	chr22:28741600-28759000	Weak transcription	Fetal Stomach	stomach
3	chr22:28742800-28759600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr22:28743000-28759000	Weak transcription	Dnd41	blood
5	chr22:28745200-28754400	Weak transcription	Brain Anterior Caudate	brain
6	chr22:28746200-28754200	Weak transcription	Fetal Heart	heart
7	chr22:28748000-28755800	Weak transcription	Fetal Intestine Small	intestine
8	chr22:28748000-28759600	Weak transcription	Fetal Lung	lung
9	chr22:28748200-28754200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr22:28748800-28754200	Weak transcription	Fetal Brain Male	brain
11	chr22:28751200-28752600	Weak transcription	Right Ventricle	heart
12	chr22:28751600-28752800	Enhancers	Fetal Brain Female	brain
13	chr22:28751600-28752800	Enhancers	Ovary	ovary
14	chr22:28752000-28754400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:28752200-28752600	Weak transcription	Left Ventricle	heart
16	chr22:28752400-28754000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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