Variant report

Variant	rs678962
Chromosome Location	chr1:172189889-172189890
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10489289	1.00[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489290	1.00[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs10489291	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10489292	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10752914	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797881	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797902	0.92[EUR][1000 genomes]
rs10911323	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911326	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911335	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911336	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911338	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911349	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911356	0.92[EUR][1000 genomes]
rs10911394	0.91[EUR][1000 genomes]
rs10911433	0.92[EUR][1000 genomes]
rs10911504	0.89[EUR][1000 genomes]
rs11583757	0.92[EUR][1000 genomes]
rs12063247	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073843	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075079	1.00[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs12081408	0.91[EUR][1000 genomes]
rs12082431	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]
rs12402454	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402792	0.86[EUR][1000 genomes]
rs12403844	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12404267	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12404363	0.86[EUR][1000 genomes]
rs12404490	0.88[EUR][1000 genomes]
rs12407453	0.84[EUR][1000 genomes]
rs12409279	0.91[EUR][1000 genomes]
rs12410143	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563643	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12567175	0.92[EUR][1000 genomes]
rs1317394	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16844126	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16844128	0.90[EUR][1000 genomes]
rs16844133	0.92[EUR][1000 genomes]
rs16844134	0.92[EUR][1000 genomes]
rs16844255	1.00[CEU][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2289635	1.00[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs2421994	1.00[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2422074	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2422075	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3850639	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3850640	1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3895277	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4072117	1.00[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs41516352	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4382763	1.00[CEU][hapmap];0.92[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs4484957	0.89[EUR][1000 genomes]
rs477289	0.80[JPT][hapmap]
rs479336	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs55656112	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56682471	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60866522	0.89[EUR][1000 genomes]
rs6676836	0.91[EUR][1000 genomes]
rs6678749	1.00[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs6686115	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686118	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72721163	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72721182	0.88[EUR][1000 genomes]
rs72721197	0.87[EUR][1000 genomes]

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	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv872546	chr1:172186321-172219995	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391951	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs678962	CREG1	cis	cerebellum	SCAN
rs678962	SELP	cis	cerebellum	SCAN
rs678962	SLC19A2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172188200-172190600	Enhancers	Primary hematopoietic stem cells	blood
2	chr1:172188200-172191000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:172189800-172190000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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