Variant report

Variant	rs2730948
Chromosome Location	chr12:39045328-39045329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10160990	0.88[TSI][hapmap]
rs1095573	0.89[YRI][hapmap]
rs1095576	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168117	0.86[EUR][1000 genomes]
rs11168929	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169105	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169268	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169324	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11559976	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12231800	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1486342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486343	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523119	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523120	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1615648	1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1621487	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1684397	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1684405	0.91[MEX][hapmap]
rs1719833	1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes]
rs1719847	1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2069210	1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2134398	0.84[ASN][1000 genomes]
rs2455609	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455610	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630782	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653722	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653738	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653752	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653754	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653760	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653761	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653769	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2653775	0.84[ASN][1000 genomes]
rs2730897	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730901	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2730910	0.82[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2730944	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730946	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730954	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2730955	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730957	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730964	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4354729	0.86[EUR][1000 genomes]
rs60368384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68075931	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73269131	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964753	0.86[EUR][1000 genomes]
rs8181763	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8181765	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826839	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826840	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826841	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826845	0.94[AMR][1000 genomes]
rs826846	0.86[AMR][1000 genomes]
rs826847	0.94[AMR][1000 genomes]
rs826849	1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs826853	0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826854	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs826857	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826860	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs826861	1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826862	1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826867	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs826868	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs826869	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826871	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826872	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs826878	0.89[YRI][hapmap]
rs826880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826884	0.88[TSI][hapmap]
rs826887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826890	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826893	0.81[YRI][hapmap]
rs826894	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs851933	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs862331	1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes]
rs862332	0.94[AMR][1000 genomes]
rs866120	0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	esv2757499	chr12:39041835-39045983	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv2759894	chr12:39041835-39045983	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39039400-39053000	Weak transcription	Left Ventricle	heart
2	chr12:39039800-39055800	Weak transcription	Hela-S3	cervix
3	chr12:39041400-39049400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:39043200-39049800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:39043800-39050600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:39044200-39055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:39044600-39046400	Weak transcription	Liver	Liver
8	chr12:39044600-39046400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:39044800-39046400	Weak transcription	GM12878-XiMat	blood
10	chr12:39045000-39046800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:39045200-39045800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:39045200-39045800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:39045200-39055400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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