Variant report

Variant	rs12082431
Chromosome Location	chr1:172234627-172234628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172228270..172230641-chr1:172232280..172235057,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10489289	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10752914	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10797881	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10797902	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911323	0.92[EUR][1000 genomes]
rs10911326	0.92[EUR][1000 genomes]
rs10911335	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10911336	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10911338	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10911349	0.92[EUR][1000 genomes]
rs10911356	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911394	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911433	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911504	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11583757	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12063247	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12073843	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12075079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12081408	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402454	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12402792	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12404363	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12404490	0.92[EUR][1000 genomes]
rs12407453	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12409279	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410143	0.92[EUR][1000 genomes]
rs12410416	1.00[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs12411264	1.00[CEU][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs12563643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567175	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844128	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844133	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844134	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2422074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757495	0.82[JPT][hapmap]
rs3850639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850640	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3895277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4072117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41516352	1.00[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4382763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4484957	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55656112	0.92[EUR][1000 genomes]
rs56682471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60866522	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676836	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686115	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6686118	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6701414	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6701929	0.82[CHD][hapmap]
rs678962	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72721163	0.92[EUR][1000 genomes]
rs72721182	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72721197	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723204	0.82[EUR][1000 genomes]
rs7550558	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12082431	CREG1	cis	cerebellum	SCAN
rs12082431	SELP	cis	cerebellum	SCAN
rs12082431	BRP44	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172225600-172246600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172231600-172234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:172234600-172235000	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:172234600-172235600	Weak transcription	Osteobl	bone

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