Variant report

Variant	rs4779039
Chromosome Location	chr15:83317767-83317768
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr15:83317616-83317811	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83316185..83318129-chr15:83417608..83419750,3	K562	blood:
2	chr15:83315484..83318072-chr15:83348095..83350570,4	MCF-7	breast:
3	chr15:83313668..83318129-chr15:83416864..83421207,8	K562	blood:
4	chr15:83313427..83317808-chr15:83477553..83483000,6	K562	blood:
5	chr15:83316633..83319257-chr15:83348234..83350901,2	MCF-7	breast:
6	chr15:83317439..83319648-chr15:83417162..83421021,3	MCF-7	breast:
7	chr15:83315715..83320562-chr15:83347753..83351536,6	K562	blood:
8	chr15:83313759..83319278-chr15:83347483..83351536,8	K562	blood:
9	chr15:83315603..83319675-chr15:83327659..83331605,4	K562	blood:

No data

Variant related genes	Relation type
CPEB1	TF binding region
ENSG00000250988	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000156232	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10400906	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10468217	0.84[ASN][1000 genomes]
rs10906984	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1145172	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1145173	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11631963	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11633829	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637433	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11855735	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12148332	0.86[ASN][1000 genomes]
rs12438312	0.87[ASN][1000 genomes]
rs12442686	0.85[ASN][1000 genomes]
rs1259180	0.85[ASN][1000 genomes]
rs1259182	0.89[ASN][1000 genomes]
rs1259183	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267657	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1267658	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1267659	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1269134	0.90[ASN][1000 genomes]
rs12911134	0.84[ASN][1000 genomes]
rs12916980	0.96[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1313492	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1313493	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1367841	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1594511	0.96[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs17158390	0.91[ASN][1000 genomes]
rs1864699	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2099259	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2278355	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs2567635	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2567636	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2678445	0.81[ASN][1000 genomes]
rs2678448	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28374463	0.87[ASN][1000 genomes]
rs28415133	0.85[ASN][1000 genomes]
rs28667458	0.84[ASN][1000 genomes]
rs2870965	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2870966	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs28808991	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34186444	0.91[ASN][1000 genomes]
rs35934048	0.82[ASN][1000 genomes]
rs36109438	0.85[ASN][1000 genomes]
rs3970696	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4778686	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4779032	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4779041	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779044	0.96[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4779050	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4779053	0.84[ASN][1000 genomes]
rs55924160	0.91[ASN][1000 genomes]
rs57181760	0.92[ASN][1000 genomes]
rs6603032	0.89[YRI][hapmap]
rs6603033	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs698500	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7165125	0.89[ASN][1000 genomes]
rs7166248	0.84[ASN][1000 genomes]
rs7167880	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7171180	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178350	0.88[ASN][1000 genomes]
rs7181761	0.96[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7182403	0.91[ASN][1000 genomes]
rs7183881	0.90[ASN][1000 genomes]
rs7494860	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7496954	0.90[ASN][1000 genomes]
rs783520	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783521	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs783522	0.91[ASN][1000 genomes]
rs783523	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs783525	0.96[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs783526	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs783527	0.96[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs783529	0.96[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs783530	0.86[ASN][1000 genomes]
rs783531	0.85[ASN][1000 genomes]
rs783532	0.86[ASN][1000 genomes]
rs783533	0.88[ASN][1000 genomes]
rs783534	0.88[ASN][1000 genomes]
rs783535	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783536	0.87[ASN][1000 genomes]
rs783537	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs783539	0.96[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs783540	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs783543	0.96[CHB][hapmap];0.83[JPT][hapmap]
rs783545	0.84[ASN][1000 genomes]
rs803747	0.96[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs8040293	0.88[ASN][1000 genomes]
rs8043401	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9652567	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1808975	chr15:83307574-83360168	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv3434026	chr15:83314547-83318195	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3360562	chr15:83315522-83318070	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4779039	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs4779039	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83314800-83317800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:83315000-83318200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:83316400-83317800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:83316800-83317800	Flanking Active TSS	Brain Cingulate Gyrus	brain
5	chr15:83316800-83318200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:83317000-83318000	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr15:83317000-83319600	Enhancers	K562	blood
8	chr15:83317200-83317800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:83317200-83317800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr15:83317200-83318000	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr15:83317200-83318200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:83317200-83331800	Weak transcription	Gastric	stomach
13	chr15:83317200-83336200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:83317400-83317800	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr15:83317400-83318000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:83317400-83318000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr15:83317600-83317800	Enhancers	Stomach Smooth Muscle	stomach
18	chr15:83317600-83318400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:83317600-83318400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:83317600-83319200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:83317600-83320800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:83317600-83322000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:83317600-83322000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:83317600-83327800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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