Variant report

Variant	rs12712994
Chromosome Location	chr2:47732894-47732895
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10175959	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10175972	0.98[ASN][1000 genomes]
rs10179452	0.81[ASN][1000 genomes]
rs10188090	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197011	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10206575	0.97[ASN][1000 genomes]
rs10206782	0.95[ASN][1000 genomes]
rs10209369	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10495945	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11684661	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684737	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11694689	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11886591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11901645	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712993	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12991125	0.97[ASN][1000 genomes]
rs13031342	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1981927	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2059520	0.90[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs2162121	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2303424	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2347795	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3732182	0.82[ASN][1000 genomes]
rs3732183	0.82[ASN][1000 genomes]
rs3764959	0.80[ASN][1000 genomes]
rs3764960	0.81[ASN][1000 genomes]
rs3771274	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs3771275	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3771276	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3771278	0.82[ASN][1000 genomes]
rs3771279	0.81[ASN][1000 genomes]
rs3771280	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3771281	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4550716	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4583514	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4596025	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6544989	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6544990	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6707467	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6711675	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6718364	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6719539	0.82[EUR][1000 genomes]
rs6720555	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6724382	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6724876	0.84[AMR][1000 genomes]
rs6726832	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6729015	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6739590	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6744097	0.85[JPT][hapmap]
rs6746426	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748435	0.82[ASN][1000 genomes]
rs6754473	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6758327	0.85[AMR][1000 genomes]
rs6759990	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7565513	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585174	0.98[ASN][1000 genomes]
rs7586575	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7596629	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7599880	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601062	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7607312	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs876936	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs876937	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs879722	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9784092	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][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	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12712994	SIX2	cis	parietal	SCAN
rs12712994	MSH2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47729800-47733800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:47730400-47735600	Weak transcription	HUVEC	blood vessel
3	chr2:47731800-47733600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:47732200-47733000	Enhancers	Brain Hippocampus Middle	brain
5	chr2:47732200-47733200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:47732400-47733400	Weak transcription	Brain Substantia Nigra	brain
7	chr2:47732400-47734000	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:47732600-47735800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:47732600-47747800	Weak transcription	Primary T cells from cord blood	blood

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