Variant report

Variant	rs783541
Chromosome Location	chr15:83255061-83255062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1145170	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1259176	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1259177	0.88[ASN][1000 genomes]
rs12908713	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1313494	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1553885	0.86[CEU][hapmap]
rs17356528	0.81[ASN][1000 genomes]
rs2567632	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34940771	0.99[ASN][1000 genomes]
rs4779046	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4779051	0.86[CEU][hapmap]
rs62009945	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165129	0.89[ASN][1000 genomes]
rs783524	0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs783528	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs783538	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs803686	0.88[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs783541	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs783541	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs783541	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs783541	RP13-996F3.5	cis	Esophagus Mucosa	GTEx
rs783541	RP11-152F13.7	cis	lung	GTEx
rs783541	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs783541	YES1	trans	lymphoblastoid	RTeQTL
rs783541	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs783541	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL
rs783541	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr15:83253800-83255200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr15:83253800-83255200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr15:83253800-83255600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:83253800-83256000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr15:83253800-83256000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr15:83253800-83256000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr15:83253800-83256400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr15:83253800-83256800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr15:83254000-83256400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:83254200-83255800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:83254600-83255200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr15:83254800-83255800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:83254800-83268200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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