Variant report

Variant	rs11167988
Chromosome Location	chr5:146745289-146745290
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10042298	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10515581	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10515582	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10515583	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11167989	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes]
rs12513884	0.94[AMR][1000 genomes]
rs12514302	0.87[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs12518250	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes]
rs12518292	0.85[AMR][1000 genomes]
rs12519887	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12520080	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12520257	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12520436	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12522616	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12651731	0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1432838	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1432839	0.89[ASN][1000 genomes]
rs1544816	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17106470	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17106482	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17106492	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17106560	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17106572	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17106575	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17106590	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17106592	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17106597	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17106606	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17106607	0.85[ASN][1000 genomes]
rs17106709	0.89[AMR][1000 genomes]
rs1895566	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2288805	0.93[JPT][hapmap];0.89[AMR][1000 genomes]
rs2288809	0.93[JPT][hapmap];0.89[AMR][1000 genomes]
rs2304043	0.89[AMR][1000 genomes]
rs2304047	0.89[AMR][1000 genomes]
rs2895681	0.94[AMR][1000 genomes]
rs3213857	0.86[JPT][hapmap];0.89[AMR][1000 genomes]
rs3749721	0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes]
rs3792837	0.86[CHB][hapmap];0.85[AMR][1000 genomes]
rs3792840	0.86[JPT][hapmap]
rs3792841	0.81[AMR][1000 genomes]
rs3805533	0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes]
rs3805534	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs3805535	0.93[JPT][hapmap]
rs3805546	0.84[AMR][1000 genomes]
rs3816012	0.81[AMR][1000 genomes]
rs4642416	0.94[AMR][1000 genomes]
rs61405762	0.91[ASN][1000 genomes]
rs73262265	0.91[ASN][1000 genomes]
rs7714240	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs972302	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146733800-146750800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:146739200-146749400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:146741800-146745600	Weak transcription	Stomach Mucosa	stomach
4	chr5:146742800-146745800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:146743200-146749600	Weak transcription	Aorta	Aorta
6	chr5:146744400-146750400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:146744600-146746000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:146745200-146745800	Enhancers	Ovary	ovary

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