Variant report

Variant	rs4779054
Chromosome Location	chr15:83375257-83375258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10400906	0.82[ASN][1000 genomes]
rs10906984	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631963	0.86[AFR][1000 genomes]
rs11633829	0.81[ASN][1000 genomes]
rs11637433	0.83[ASN][1000 genomes]
rs11855735	0.81[ASN][1000 genomes]
rs12438312	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12442686	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1259182	0.80[ASN][1000 genomes]
rs1269134	0.81[ASN][1000 genomes]
rs12911134	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12916980	0.83[ASN][1000 genomes]
rs1367841	0.83[ASN][1000 genomes]
rs1594511	0.83[ASN][1000 genomes]
rs17158390	0.83[ASN][1000 genomes]
rs1864699	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2099259	0.83[ASN][1000 genomes]
rs2278355	0.86[AFR][1000 genomes]
rs28667458	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2870966	0.83[ASN][1000 genomes]
rs34186444	0.83[ASN][1000 genomes]
rs4778686	0.83[ASN][1000 genomes]
rs4779041	0.83[ASN][1000 genomes]
rs4779044	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779050	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779053	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55924160	0.83[ASN][1000 genomes]
rs57181760	0.81[ASN][1000 genomes]
rs6603033	0.83[ASN][1000 genomes]
rs7165125	0.81[ASN][1000 genomes]
rs7166248	0.81[ASN][1000 genomes]
rs7167880	0.83[ASN][1000 genomes]
rs7171180	0.83[ASN][1000 genomes]
rs7178350	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7182403	0.82[ASN][1000 genomes]
rs7183881	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7494860	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7496954	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783520	0.81[ASN][1000 genomes]
rs783521	0.83[ASN][1000 genomes]
rs783522	0.83[ASN][1000 genomes]
rs783523	0.83[ASN][1000 genomes]
rs783525	0.83[ASN][1000 genomes]
rs783526	0.81[ASN][1000 genomes]
rs783527	0.81[ASN][1000 genomes]
rs8040293	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8043401	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9652567	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS 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
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS 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
11	nsv904450	chr15:83347193-83395340	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4779054	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs4779054	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs4779054	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83349800-83377200	Weak transcription	Brain Anterior Caudate	brain
2	chr15:83351600-83377200	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:83351800-83377200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:83351800-83377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:83358200-83377200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83365400-83376600	Weak transcription	Fetal Brain Male	brain
7	chr15:83368400-83376800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:83368400-83377400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:83368600-83377000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:83368800-83377600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:83369000-83376000	Weak transcription	Fetal Brain Female	brain
12	chr15:83369000-83376600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:83369000-83376800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:83369000-83376800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:83370200-83376600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:83371000-83376600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:83371600-83376800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:83373400-83376000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:83374800-83376000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:83374800-83377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:83375000-83377200	Weak transcription	HMEC	breast
22	chr15:83375200-83375400	Enhancers	HUES48 Cell Line	embryonic stem cell

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