Variant report

Variant	rs378858
Chromosome Location	chr5:58685322-58685323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs165940	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs168641	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16889733	0.96[EUR][1000 genomes]
rs171801	0.86[JPT][hapmap]
rs181736	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs185417	0.91[ASN][1000 genomes]
rs187368	0.96[EUR][1000 genomes]
rs193447	0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2441091	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244579	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244580	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244582	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244583	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244587	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs244590	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244591	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]
rs244592	0.91[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs244593	0.95[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs244594	0.96[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs244595	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs244596	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs244597	0.96[CEU][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes]
rs258106	0.86[JPT][hapmap]
rs258110	0.86[JPT][hapmap]
rs258111	0.86[JPT][hapmap]
rs258112	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs258113	0.91[ASN][1000 genomes]
rs258114	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs258115	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs258116	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258117	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258118	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258122	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258126	0.88[ASN][1000 genomes]
rs258127	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs258128	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2591750	0.83[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs365223	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371775	0.85[JPT][hapmap]
rs378869	0.86[JPT][hapmap]
rs378970	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs380993	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]
rs381755	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs383046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392901	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs401013	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs403672	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];0.99[ASN][1000 genomes]
rs403695	1.00[CEU][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs424839	1.00[CEU][hapmap];0.96[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]
rs427433	0.96[EUR][1000 genomes]
rs427740	0.86[JPT][hapmap]
rs427748	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs428059	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs431645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432879	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433161	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs433565	0.86[JPT][hapmap]
rs434183	0.93[EUR][1000 genomes]
rs434274	0.94[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434422	0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs441817	0.96[EUR][1000 genomes]
rs444552	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs454702	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573336	0.85[JPT][hapmap]
rs611540	0.85[EUR][1000 genomes]
rs611541	0.85[EUR][1000 genomes]
rs669240	0.83[CHB][hapmap];0.86[JPT][hapmap]

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:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58672200-58689200	Weak transcription	Fetal Brain Female	brain
2	chr5:58676400-58686200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:58682000-58711800	Weak transcription	Psoas Muscle	Psoas
4	chr5:58683200-58686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:58683800-58691600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:58684400-58697600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58684600-58686400	Weak transcription	A549	lung

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