Variant report

Variant	rs783539
Chromosome Location	chr15:83254070-83254071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83251945..83254167-chr15:83721168..83723752,2	K562	blood:
2	chr15:83254004..83256301-chr15:83611241..83613482,2	MCF-7	breast:
3	chr15:83253377..83255551-chr15:83668447..83670798,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10400906	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10468217	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10906984	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1145172	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1145173	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11631963	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11633829	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11635624	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11637433	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11855735	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12148332	0.97[ASN][1000 genomes]
rs12438312	0.89[ASN][1000 genomes]
rs12442686	0.87[ASN][1000 genomes]
rs1259180	0.96[ASN][1000 genomes]
rs1259182	0.93[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1267657	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1267658	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1267659	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1269134	0.92[ASN][1000 genomes]
rs12911134	0.86[ASN][1000 genomes]
rs12916980	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1313492	0.97[ASN][1000 genomes]
rs1313493	0.97[ASN][1000 genomes]
rs1367841	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1594511	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17158390	0.93[ASN][1000 genomes]
rs17158403	0.87[YRI][hapmap]
rs17356118	0.95[YRI][hapmap]
rs1864699	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2099259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278355	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs2567635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2567636	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2678445	0.90[ASN][1000 genomes]
rs2678448	0.97[ASN][1000 genomes]
rs28374463	0.89[ASN][1000 genomes]
rs28415133	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28667458	0.86[ASN][1000 genomes]
rs2870965	0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2870966	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs28808991	0.99[ASN][1000 genomes]
rs34186444	0.93[ASN][1000 genomes]
rs35934048	0.92[ASN][1000 genomes]
rs36109438	0.97[ASN][1000 genomes]
rs3970696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4778686	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4779032	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4779039	0.96[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4779041	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4779050	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4779053	0.86[ASN][1000 genomes]
rs55924160	0.93[ASN][1000 genomes]
rs57181760	0.92[ASN][1000 genomes]
rs62009923	0.88[EUR][1000 genomes]
rs6603033	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs698500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7165125	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166248	0.86[ASN][1000 genomes]
rs7167880	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7171180	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7178350	0.90[ASN][1000 genomes]
rs7181761	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7182403	0.92[ASN][1000 genomes]
rs7183881	0.92[ASN][1000 genomes]
rs7494860	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7496954	0.92[ASN][1000 genomes]
rs783520	0.92[ASN][1000 genomes]
rs783521	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs783522	0.93[ASN][1000 genomes]
rs783523	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs783525	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs783526	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs783527	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs783529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs783530	0.97[ASN][1000 genomes]
rs783531	0.95[ASN][1000 genomes]
rs783532	0.97[ASN][1000 genomes]
rs783533	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783534	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783535	0.95[ASN][1000 genomes]
rs783536	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs783537	0.95[ASN][1000 genomes]
rs783540	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs783543	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs783545	0.95[ASN][1000 genomes]
rs803687	0.89[ASN][1000 genomes]
rs803688	0.90[ASN][1000 genomes]
rs803747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8040293	0.90[ASN][1000 genomes]
rs8043401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9652567	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

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	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs783539	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs783539	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs783539	GOLGA6L10	cis	Esophagus Muscularis	GTEx
rs783539	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs783539	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs783539	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83241800-83297600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:83253000-83254200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:83253600-83254800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:83253800-83254200	Enhancers	Adipose Nuclei	Adipose
5	chr15:83253800-83254400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:83253800-83254400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:83253800-83254400	Enhancers	Osteobl	bone
8	chr15:83253800-83254600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr15:83253800-83254600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:83253800-83255200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr15:83253800-83255200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr15:83253800-83255600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:83253800-83256000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:83253800-83256000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr15:83253800-83256000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr15:83253800-83256400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr15:83253800-83256800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:83254000-83254200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr15:83254000-83254200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
20	chr15:83254000-83254400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:83254000-83254400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:83254000-83254600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:83254000-83256400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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