Variant report

Variant	rs2291365
Chromosome Location	chr12:25272027-25272028
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	chr12:25144178..25145423-chr12:25271630..25272711,4	MCF-7	breast:
2	chr12:25005092..25005668-chr12:25271970..25272610,3	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10505960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10505980	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10771169	0.92[AFR][1000 genomes]
rs10771171	0.82[AFR][1000 genomes]
rs10771174	0.90[ASN][1000 genomes]
rs10771177	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10842466	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10842471	0.92[AFR][1000 genomes]
rs10842473	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10842475	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10842478	0.82[AFR][1000 genomes]
rs10842490	0.83[AFR][1000 genomes]
rs10842491	0.83[AFR][1000 genomes]
rs10842492	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10842493	0.90[ASN][1000 genomes]
rs10842494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10842496	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10842498	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10842501	0.84[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs10842502	0.83[JPT][hapmap]
rs10842504	0.92[JPT][hapmap]
rs10842505	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10842514	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs11047824	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs11047846	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047849	0.94[ASN][1000 genomes]
rs11047852	0.82[AFR][1000 genomes]
rs11047854	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047855	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11047856	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11047865	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11047868	0.88[ASN][1000 genomes]
rs11047870	0.86[ASN][1000 genomes]
rs11047887	0.84[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap]
rs11047888	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11047894	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11047901	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11047902	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11047915	0.83[JPT][hapmap]
rs11047919	0.83[JPT][hapmap]
rs1137188	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11513449	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611468	0.81[CHB][hapmap]
rs11832421	0.95[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap]
rs12226937	0.83[JPT][hapmap]
rs12228638	0.84[ASW][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12368504	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12423443	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs12424685	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425900	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12579073	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12579942	0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs12581134	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12587	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12810577	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs12813551	0.83[JPT][hapmap]
rs12814442	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12815546	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12818169	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12822857	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs12828225	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12828609	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12830058	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12830336	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13096	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs17329025	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1908946	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2352782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2352784	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34898174	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4246229	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs4559767	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4589388	0.83[AFR][1000 genomes]
rs4963848	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4963850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4963859	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4963860	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs61020746	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487456	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487464	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs712	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7133904	0.92[AFR][1000 genomes]
rs7297103	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7298636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7299998	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7302922	0.84[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap]
rs7306769	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7308865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7309124	0.83[ASN][1000 genomes]
rs7971062	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7971288	0.84[ASW][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9266	0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs9634100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv557796	chr12:25266203-25306458	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2291365	LYRM5	cis	parietal	SCAN
rs2291365	GOLT1B	cis	parietal	SCAN
rs2291365	PYROXD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
2	chr12:25263800-25288800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:25268600-25279400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links