Variant report

Variant	rs28454949
Chromosome Location	chr15:82562367-82562368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11073036	0.87[ASN][1000 genomes]
rs11630197	0.84[ASN][1000 genomes]
rs11631813	0.86[ASN][1000 genomes]
rs11633000	0.90[ASN][1000 genomes]
rs11854289	0.94[ASN][1000 genomes]
rs11854483	0.94[ASN][1000 genomes]
rs12324875	0.82[ASN][1000 genomes]
rs1501367	0.96[ASN][1000 genomes]
rs1566559	0.95[ASN][1000 genomes]
rs1566560	0.95[ASN][1000 genomes]
rs1566561	0.82[ASN][1000 genomes]
rs16973457	0.94[ASN][1000 genomes]
rs1846908	0.95[ASN][1000 genomes]
rs1948741	0.87[ASN][1000 genomes]
rs1948742	0.86[ASN][1000 genomes]
rs1972460	0.87[ASN][1000 genomes]
rs2016372	0.83[ASN][1000 genomes]
rs2047679	0.97[ASN][1000 genomes]
rs28522807	0.94[ASN][1000 genomes]
rs28564699	0.85[ASN][1000 genomes]
rs28610286	0.88[ASN][1000 genomes]
rs3759800	0.97[ASN][1000 genomes]
rs3858953	0.83[ASN][1000 genomes]
rs3902959	0.97[ASN][1000 genomes]
rs4238534	0.86[ASN][1000 genomes]
rs4267268	0.81[ASN][1000 genomes]
rs4296215	0.86[ASN][1000 genomes]
rs4778674	0.92[ASN][1000 genomes]
rs4778986	0.82[ASN][1000 genomes]
rs4778987	0.84[ASN][1000 genomes]
rs4778990	0.92[ASN][1000 genomes]
rs56398167	0.87[ASN][1000 genomes]
rs61554133	0.86[ASN][1000 genomes]
rs62012054	0.84[ASN][1000 genomes]
rs62012055	0.86[ASN][1000 genomes]
rs7167504	0.88[ASN][1000 genomes]
rs7176926	0.97[ASN][1000 genomes]
rs72749564	0.81[ASN][1000 genomes]
rs72749575	0.83[ASN][1000 genomes]
rs72749586	0.83[ASN][1000 genomes]
rs7403041	0.92[ASN][1000 genomes]
rs7403244	0.92[ASN][1000 genomes]
rs8025964	0.87[ASN][1000 genomes]
rs8030210	0.87[ASN][1000 genomes]
rs8030250	0.87[ASN][1000 genomes]
rs8032633	0.87[ASN][1000 genomes]
rs8033313	0.84[ASN][1000 genomes]
rs9972440	0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28454949	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs28454949	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs28454949	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82555400-82565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:82555800-82566400	Weak transcription	Ovary	ovary
3	chr15:82556000-82563200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:82556000-82566400	Weak transcription	Fetal Lung	lung
5	chr15:82556200-82567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:82559600-82564000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:82559600-82567400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:82561000-82562400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:82561200-82564000	Weak transcription	K562	blood
10	chr15:82561200-82568400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:82561400-82568000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:82561600-82562400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr15:82561600-82562400	Enhancers	NHEK	skin
14	chr15:82561800-82562600	Enhancers	HMEC	breast
15	chr15:82561800-82563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:82561800-82565400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:82561800-82569400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:82562000-82563200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:82562000-82566400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:82562200-82566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:82562200-82567600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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