Variant report

Variant	rs1297607
Chromosome Location	chr22:28719656-28719657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10212083	0.91[CEU][hapmap]
rs10483148	1.00[CHB][hapmap]
rs10483150	1.00[CHB][hapmap]
rs10483151	0.83[CEU][hapmap]
rs12166475	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]
rs12167532	0.82[EUR][1000 genomes]
rs12167735	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs12170637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[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];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
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];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap];0.87[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];0.90[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs135641	1.00[CHB][hapmap]
rs135642	1.00[CHB][hapmap]
rs135644	1.00[CHB][hapmap]
rs135645	1.00[CHB][hapmap]
rs135649	1.00[CHB][hapmap]
rs1569700	1.00[CHB][hapmap]
rs16986077	1.00[MEX][hapmap]
rs16986177	1.00[CHB][hapmap]
rs16986254	1.00[CHB][hapmap]
rs16986257	1.00[CHB][hapmap]
rs16986266	1.00[CHB][hapmap]
rs16986308	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16986398	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]
rs17413461	0.83[CEU][hapmap]
rs17487463	0.83[CEU][hapmap]
rs56391942	0.87[AFR][1000 genomes]
rs7285440	1.00[CHB][hapmap]
rs7289625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7291268	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs73430118	0.82[EUR][1000 genomes]
rs738200	0.91[CEU][hapmap];1.00[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];0.87[GIH][hapmap];1.00[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]
rs9625433	0.83[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs9625437	0.91[CEU][hapmap]
rs9625438	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
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];0.83[YRI][hapmap]
rs9625478	0.83[CEU][hapmap]

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	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
4	nsv526760	chr22:28706220-28719656	Enhancers Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1297607	TTC28	cis	lymphoblastoid	seeQTL
rs1297607	TFIP11	cis	cerebellum	SCAN
rs1297607	TMEM211	cis	cerebellum	SCAN
rs1297607	TXNDC2	trans	cerebellum	SCAN
rs1297607	C22orf15	cis	cerebellum	SCAN
rs1297607	GAL3ST1	cis	cerebellum	SCAN
rs1297607	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28712200-28725600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:28716400-28722600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr22:28717200-28726400	Weak transcription	Brain Germinal Matrix	brain

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