Variant report

Variant	rs1551564
Chromosome Location	chr5:58734162-58734163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10514864	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs1156028	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs12518641	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457112	0.97[ASN][1000 genomes]
rs16889853	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs16889892	0.85[JPT][hapmap]
rs16889901	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16889903	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs16889904	0.85[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs174039	0.80[JPT][hapmap]
rs2112910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505532	0.97[ASN][1000 genomes]
rs28666954	1.00[ASN][1000 genomes]
rs28729916	1.00[ASN][1000 genomes]
rs3852147	0.86[JPT][hapmap]
rs41447947	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs58232524	1.00[ASN][1000 genomes]
rs59152084	1.00[ASN][1000 genomes]
rs59246284	0.96[ASN][1000 genomes]
rs60509830	1.00[ASN][1000 genomes]
rs6870632	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs988827	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs988828	0.95[CEU][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][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	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
4	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
5	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
6	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
7	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
3	chr5:58716000-58756600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58719400-58738400	Weak transcription	Fetal Intestine Small	intestine
5	chr5:58728000-58735200	Strong transcription	A549	lung
6	chr5:58731000-58735200	Enhancers	Fetal Brain Male	brain
7	chr5:58731400-58734600	Enhancers	Fetal Lung	lung
8	chr5:58731400-58735000	Weak transcription	Psoas Muscle	Psoas
9	chr5:58731800-58734200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr5:58731800-58735400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:58731800-58764800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:58732000-58740000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:58732800-58735000	Enhancers	Colon Smooth Muscle	Colon
14	chr5:58733400-58738200	Weak transcription	Fetal Brain Female	brain

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