Variant report

Variant	rs244590
Chromosome Location	chr5:58677945-58677946
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs165940	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs168641	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16889733	0.96[EUR][1000 genomes]
rs181736	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs185417	0.91[ASN][1000 genomes]
rs187368	0.96[EUR][1000 genomes]
rs193447	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs2441091	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244579	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244580	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244582	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244583	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244587	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244591	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244592	0.86[CEU][hapmap];0.96[EUR][1000 genomes]
rs244593	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs244594	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs244595	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs244596	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs244597	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs258112	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs258113	0.91[ASN][1000 genomes]
rs258114	0.91[ASN][1000 genomes]
rs258115	0.91[ASN][1000 genomes]
rs258116	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258117	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258118	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258122	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258126	0.88[ASN][1000 genomes]
rs258127	0.88[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs258128	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2591750	0.83[CHB][hapmap];0.97[ASN][1000 genomes]
rs365223	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368538	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370891	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371775	0.84[CHB][hapmap]
rs378858	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]
rs378970	0.83[CHB][hapmap]
rs380993	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]
rs381755	0.84[CHB][hapmap]
rs383046	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387647	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392901	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs401013	0.84[CHB][hapmap]
rs403672	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs403695	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs424839	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427433	0.96[EUR][1000 genomes]
rs427740	0.84[CHB][hapmap]
rs427748	0.84[CHB][hapmap]
rs428059	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs431645	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432879	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433161	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs434183	0.94[EUR][1000 genomes]
rs434274	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434422	0.96[EUR][1000 genomes]
rs441817	0.96[EUR][1000 genomes]
rs444552	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs454702	0.95[CEU][hapmap];0.84[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530656	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531511	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573336	0.84[CHB][hapmap]
rs611540	0.86[EUR][1000 genomes]
rs611541	0.85[EUR][1000 genomes]
rs669240	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:12 , 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	chr5:58676200-58678000	Enhancers	Fetal Intestine Small	intestine
6	chr5:58676200-58678200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:58676200-58678400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:58676400-58681600	Enhancers	A549	lung
9	chr5:58676400-58686200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:58677400-58678000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:58677400-58678200	Enhancers	Fetal Brain Male	brain
12	chr5:58677800-58678000	Enhancers	Fetal Lung	lung

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