Variant report

Variant	rs165940
Chromosome Location	chr5:58679484-58679485
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs168641	0.83[EUR][1000 genomes]
rs16889733	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs171800	0.91[ASN][1000 genomes]
rs171801	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs181736	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs187368	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187716	0.90[ASN][1000 genomes]
rs193447	0.84[JPT][hapmap]
rs2441091	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs244568	0.86[CHB][hapmap]
rs244579	0.83[EUR][1000 genomes]
rs244580	0.83[EUR][1000 genomes]
rs244582	0.83[EUR][1000 genomes]
rs244583	0.83[EUR][1000 genomes]
rs244587	0.83[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs244590	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs244591	0.95[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes]
rs244592	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244593	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244595	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244597	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258104	0.97[ASN][1000 genomes]
rs258105	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs258106	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs258108	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs258109	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs258110	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs258111	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs258116	0.90[EUR][1000 genomes]
rs258117	0.90[EUR][1000 genomes]
rs258118	0.90[EUR][1000 genomes]
rs258122	0.82[EUR][1000 genomes]
rs258127	0.90[JPT][hapmap]
rs258128	0.95[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs258129	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2591750	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2607343	0.96[ASN][1000 genomes]
rs365223	0.94[EUR][1000 genomes]
rs368538	0.96[EUR][1000 genomes]
rs370891	0.96[EUR][1000 genomes]
rs371775	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs378858	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs378869	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs378970	0.86[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs380118	0.97[ASN][1000 genomes]
rs380993	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs381755	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs383046	0.96[EUR][1000 genomes]
rs383444	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs387647	0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs392901	0.83[JPT][hapmap]
rs401013	0.87[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs403672	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs403695	0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs419744	0.94[ASN][1000 genomes]
rs419953	0.97[ASN][1000 genomes]
rs424839	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs427433	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427740	0.87[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs427748	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs428059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429191	0.97[ASN][1000 genomes]
rs431645	0.96[EUR][1000 genomes]
rs432879	0.91[EUR][1000 genomes]
rs433161	0.94[ASW][hapmap];1.00[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];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433565	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs434183	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434274	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs434422	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441817	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443191	0.97[ASN][1000 genomes]
rs444552	0.94[ASW][hapmap];1.00[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];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454702	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes]
rs487029	0.88[ASN][1000 genomes]
rs530656	0.96[EUR][1000 genomes]
rs531511	0.96[EUR][1000 genomes]
rs573230	0.95[ASN][1000 genomes]
rs573336	0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs575045	0.97[ASN][1000 genomes]
rs611540	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs611541	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62355534	0.92[ASN][1000 genomes]
rs62355535	0.92[ASN][1000 genomes]
rs62355536	0.88[ASN][1000 genomes]
rs651576	0.89[ASN][1000 genomes]
rs669240	0.86[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs670169	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58666000-58681400	Weak transcription	Psoas Muscle	Psoas
2	chr5:58672200-58689200	Weak transcription	Fetal Brain Female	brain
3	chr5:58672800-58681600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:58675400-58681400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:58676400-58681600	Enhancers	A549	lung
6	chr5:58676400-58686200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:58678000-58683000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:58678400-58681400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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