Variant report

Variant	rs134514
Chromosome Location	chr22:28762034-28762035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10212083	0.91[CEU][hapmap]
rs10483148	1.00[CHB][hapmap]
rs10483150	1.00[CHB][hapmap]
rs10483151	0.83[CEU][hapmap]
rs12165715	0.85[AMR][1000 genomes]
rs12166245	0.87[AMR][1000 genomes]
rs12166475	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]
rs12167122	0.87[AMR][1000 genomes]
rs12167532	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12167735	0.86[GIH][hapmap];0.88[MEX][hapmap]
rs12169120	0.85[AMR][1000 genomes]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs1297607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134194	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs134197	0.83[CEU][hapmap];0.88[MEX][hapmap]
rs134488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134501	1.00[CHB][hapmap]
rs134503	1.00[CHB][hapmap]
rs134504	1.00[CHB][hapmap]
rs134506	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]
rs134509	1.00[CHB][hapmap]
rs134510	1.00[CHB][hapmap]
rs134520	1.00[CHB][hapmap]
rs134521	1.00[CHB][hapmap]
rs134524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134528	1.00[CHB][hapmap]
rs134547	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]
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	0.87[EUR][1000 genomes]
rs16986398	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]
rs16986509	0.91[CEU][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap]
rs17413461	0.83[CEU][hapmap]
rs17487463	0.83[CEU][hapmap]
rs2013784	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2144922	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2881496	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58542867	0.87[AMR][1000 genomes]
rs6005807	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs6005809	0.83[AMR][1000 genomes]
rs60065194	0.87[AMR][1000 genomes]
rs7285440	1.00[CHB][hapmap]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7291268	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs73430118	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73430168	0.83[AMR][1000 genomes]
rs73430179	0.87[AMR][1000 genomes]
rs73430189	0.85[AMR][1000 genomes]
rs738200	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs79104	1.00[CHB][hapmap]
rs79107	1.00[CHB][hapmap]
rs9306457	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs9620778	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs9620779	0.91[CEU][hapmap]
rs9620797	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs9620799	0.83[YRI][hapmap]
rs9620804	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs9620808	0.87[AMR][1000 genomes]
rs9625433	0.83[CEU][hapmap];0.88[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];0.88[MEX][hapmap]
rs9625477	0.91[CEU][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap]
rs9625478	0.83[CEU][hapmap]
rs9625498	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9625509	0.87[AMR][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
rs134514	TTC28	cis	lymphoblastoid	seeQTL
rs134514	GAL3ST1	cis	cerebellum	SCAN
rs134514	C22orf15	cis	cerebellum	SCAN
rs134514	TXNDC2	trans	cerebellum	SCAN
rs134514	SEZ6L	cis	cerebellum	SCAN
rs134514	TFIP11	cis	cerebellum	SCAN
rs134514	TMEM211	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28752800-28768600	Weak transcription	Left Ventricle	heart
2	chr22:28754800-28766000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr22:28759600-28763600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:28759800-28766000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr22:28759800-28777200	Weak transcription	Fetal Stomach	stomach
6	chr22:28760000-28766000	Weak transcription	Psoas Muscle	Psoas
7	chr22:28760000-28766000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr22:28760000-28771800	Weak transcription	Right Ventricle	heart
9	chr22:28760200-28768800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:28761800-28762200	Strong transcription	Dnd41	blood

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