Variant report

Variant	rs7297103
Chromosome Location	chr12:25265295-25265296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10505960	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10505980	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs10771174	0.81[ASN][1000 genomes]
rs10771177	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10842466	0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10842473	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10842475	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10842492	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10842493	0.81[ASN][1000 genomes]
rs10842494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10842496	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10842498	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10842501	0.84[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs10842502	0.84[JPT][hapmap]
rs10842504	0.92[JPT][hapmap]
rs10842505	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs10842514	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11047823	0.85[ASN][1000 genomes]
rs11047824	0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11047846	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047849	0.84[ASN][1000 genomes]
rs11047854	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047855	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11047856	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11047865	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11047887	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs11047888	0.84[CHB][hapmap];0.81[CHD][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	0.84[JPT][hapmap]
rs11047919	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs1137188	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11513449	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611468	0.81[CHB][hapmap]
rs11832421	0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11832456	0.83[ASN][1000 genomes]
rs12226937	0.84[JPT][hapmap]
rs12368504	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12423443	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs12424685	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12425900	0.88[EUR][1000 genomes];0.94[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];0.84[JPT][hapmap]
rs12581134	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12587	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12810577	0.84[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap]
rs12813551	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs12814442	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12815546	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12818169	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12822857	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs12828225	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12828609	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12830058	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12830336	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13096	0.84[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs17329025	0.84[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap]
rs1908946	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2291365	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]
rs2352782	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352784	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4246229	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs4559767	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4963848	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4963850	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4963859	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4963860	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs61020746	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6487456	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487464	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs712	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7298636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7299998	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7302922	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs7306769	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7308865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9266	0.84[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs9634100	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7297103	LYRM5	cis	parietal	SCAN
rs7297103	PYROXD1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
2	chr12:25261000-25268400	Weak transcription	Liver	Liver
3	chr12:25262800-25266200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:25263200-25266000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:25263600-25265400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:25263600-25265400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:25263600-25267600	Weak transcription	Thymus	Thymus
8	chr12:25263600-25268600	Weak transcription	GM12878-XiMat	blood
9	chr12:25263800-25265400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:25263800-25265400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:25263800-25265600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:25263800-25267400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:25263800-25288800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:25264000-25265800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:25264400-25266000	Weak transcription	Primary B cells from cord blood	blood
16	chr12:25264400-25266000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:25264600-25266200	Weak transcription	Fetal Thymus	thymus
18	chr12:25265000-25266600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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