Variant report

Variant	rs7728100
Chromosome Location	chr5:59553708-59553709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10051717	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064516	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10074696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10077172	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471474	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471475	0.82[YRI][hapmap]
rs12516794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520400	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12523473	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[ASN][1000 genomes]
rs1559276	1.00[JPT][hapmap]
rs4328990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404639	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410606	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4604150	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4700370	0.89[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59518781	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60399456	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62370659	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62371960	0.97[ASN][1000 genomes]
rs6862158	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72755103	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7444733	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7714765	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9291685	0.83[ASW][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv4847	chr5:59523591-59569307	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv969227	chr5:59550035-59556265	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7728100	SLC2A4	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59546400-59555200	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59551400-59554400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:59552400-59554200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:59553200-59554000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr5:59553200-59554400	Enhancers	HepG2	liver
6	chr5:59553400-59553800	Enhancers	Fetal Lung	lung
7	chr5:59553400-59554200	Enhancers	Brain Cingulate Gyrus	brain
8	chr5:59553400-59554200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr5:59553400-59554200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr5:59553600-59554000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:59553600-59554000	Enhancers	Adipose Nuclei	Adipose
12	chr5:59553600-59554000	Enhancers	Brain Substantia Nigra	brain
13	chr5:59553600-59554000	Enhancers	Fetal Brain Female	brain
14	chr5:59553600-59554200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:59553600-59554400	Enhancers	Fetal Brain Male	brain

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