Variant report

Variant	rs401013
Chromosome Location	chr5:58689199-58689200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs165940	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs16889733	0.96[ASN][1000 genomes]
rs171800	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs171801	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs187368	0.97[ASN][1000 genomes]
rs187716	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs193447	0.89[JPT][hapmap]
rs244586	0.83[EUR][1000 genomes]
rs244590	0.84[CHB][hapmap]
rs244591	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs244592	0.87[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs244593	0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs244594	0.87[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs244595	0.90[CHB][hapmap];0.80[JPT][hapmap];0.97[ASN][1000 genomes]
rs244596	0.87[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs244597	0.86[CHB][hapmap];0.97[ASN][1000 genomes]
rs258104	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258105	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258106	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258108	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258109	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258110	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258111	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258127	0.89[JPT][hapmap]
rs258128	0.89[JPT][hapmap]
rs258129	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2591750	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2607343	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs371775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378858	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs378869	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380118	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380993	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs381755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383444	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387647	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs392901	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs403672	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs403695	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs419744	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419953	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424839	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs427433	0.97[ASN][1000 genomes]
rs427740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs427748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs428059	0.86[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs429191	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs433161	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs433565	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434183	0.97[ASN][1000 genomes]
rs434422	0.87[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs441817	0.97[ASN][1000 genomes]
rs443191	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444552	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs454702	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs487029	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs573230	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs573336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs575045	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611540	0.89[ASN][1000 genomes]
rs611541	0.90[ASN][1000 genomes]
rs62355534	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62355535	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62355536	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs651576	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs669240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670169	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1032887	chr5:58678623-58690251	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58672200-58689200	Weak transcription	Fetal Brain Female	brain
2	chr5:58682000-58711800	Weak transcription	Psoas Muscle	Psoas
3	chr5:58683800-58691600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:58684400-58697600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:58687400-58689800	Weak transcription	Fetal Brain Male	brain
6	chr5:58688800-58690200	Strong transcription	A549	lung

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