Variant report

Variant	rs4778989
Chromosome Location	chr15:82569304-82569305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11548681	0.90[ASN][1000 genomes]
rs16973456	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17269819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470877	0.85[EUR][1000 genomes]
rs28542747	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587326	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867634	0.84[AMR][1000 genomes]
rs2867649	0.84[EUR][1000 genomes]
rs28689861	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28697264	0.89[EUR][1000 genomes]
rs35462466	0.90[ASN][1000 genomes]
rs4778979	0.90[ASN][1000 genomes]
rs4778984	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010071	0.85[EUR][1000 genomes]
rs62012011	0.80[EUR][1000 genomes]
rs62012046	0.84[EUR][1000 genomes]
rs62012047	0.84[EUR][1000 genomes]
rs62012049	0.84[EUR][1000 genomes]
rs62012056	0.87[EUR][1000 genomes]
rs62012059	0.87[EUR][1000 genomes]
rs62013461	0.86[EUR][1000 genomes]
rs62013464	0.83[EUR][1000 genomes]
rs7165536	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168667	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs7496227	0.87[EUR][1000 genomes]
rs8026737	0.85[EUR][1000 genomes]
rs8034801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042461	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9944185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv904442	chr15:82540174-82571046	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv904443	chr15:82553472-82571780	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4778989	AP3B2	cis	lung	GTEx
rs4778989	AP3B2	cis	Nerve Tibial	GTEx
rs4778989	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs4778989	AP3B2	cis	Muscle Skeletal	GTEx
rs4778989	AP3B2	cis	Artery Tibial	GTEx
rs4778989	RP11-152F13.3	cis	lung	GTEx
rs4778989	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs4778989	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4778989	RP13-608F4.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82561800-82569400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:82564800-82570000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:82566800-82569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:82568400-82569600	Weak transcription	Fetal Lung	lung

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