Variant report

Variant	rs12475441
Chromosome Location	chr2:63485054-63485055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10203263	0.84[ASW][hapmap];0.83[MKK][hapmap]
rs10206458	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10209822	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs10496101	1.00[YRI][hapmap]
rs11125949	1.00[YRI][hapmap]
rs11125957	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs11883730	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs12151606	1.00[LWK][hapmap];0.90[MKK][hapmap]
rs12329383	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12466601	1.00[YRI][hapmap]
rs12473198	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473894	1.00[YRI][hapmap]
rs12478442	1.00[YRI][hapmap]
rs13411767	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13417792	0.84[ASW][hapmap];0.83[MKK][hapmap]
rs13422328	0.80[MKK][hapmap]
rs1400686	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs1517405	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs1517406	0.86[ASW][hapmap];0.81[CEU][hapmap];0.95[CHD][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1517407	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1517408	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607205	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs17348120	0.89[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs17348207	1.00[YRI][hapmap]
rs17408652	1.00[LWK][hapmap];0.81[MKK][hapmap]
rs17408750	0.92[ASN][1000 genomes]
rs17408841	0.88[LWK][hapmap]
rs17408988	0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs17474666	1.00[YRI][hapmap]
rs1829526	1.00[YRI][hapmap]
rs2090479	0.84[ASW][hapmap];0.85[LWK][hapmap]
rs2138799	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2176418	0.87[LWK][hapmap]
rs2263636	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs2292794	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs2292795	0.84[ASW][hapmap]
rs2421822	0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.99[ASN][1000 genomes]
rs2421862	0.84[ASW][hapmap];0.85[MKK][hapmap]
rs2421863	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2421879	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2459625	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2677439	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs2677443	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2699389	0.82[ASW][hapmap];0.87[LWK][hapmap]
rs2699393	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2699394	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2699396	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2699397	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901574	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2951180	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453673	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671458	1.00[YRI][hapmap]
rs4671461	1.00[YRI][hapmap]
rs4671462	0.99[ASN][1000 genomes]
rs4671474	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs4671479	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs62177760	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62177773	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62177784	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62177822	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6545984	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs6545986	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs6545997	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs6706180	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs6724044	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs6725694	0.84[ASW][hapmap];0.85[LWK][hapmap]
rs6735612	0.90[ASN][1000 genomes]
rs7558922	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs7559137	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs7561802	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs7584531	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585088	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585342	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7585664	0.84[ASW][hapmap];0.85[LWK][hapmap]
rs7591562	0.84[ASW][hapmap];0.87[LWK][hapmap]
rs7596446	0.84[ASW][hapmap]
rs7599736	0.84[ASW][hapmap]
rs992214	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs993244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1009191	chr2:63473443-63578508	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63463600-63487800	Weak transcription	Left Ventricle	heart
2	chr2:63464800-63485400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:63476600-63496000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:63484000-63487200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:63484400-63485200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:63484400-63485200	Enhancers	Adipose Nuclei	Adipose
7	chr2:63484400-63485200	Enhancers	Dnd41	blood
8	chr2:63484400-63485600	Enhancers	GM12878-XiMat	blood
9	chr2:63484800-63485200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:63485000-63485200	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:63485000-63485600	Enhancers	Primary T cells from cord blood	blood

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