Variant report

Variant	rs4777540
Chromosome Location	chr15:73078286-73078287
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESRRA	chr15:73074606-73078362	GM12878	blood:	n/a	n/a
2	ZNF143	chr15:73078180-73078312	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73074691..73078350-chr15:73341676..73346479,5	MCF-7	breast:

Variant related genes	Relation type
ADPGK	TF binding region
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11072384	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11072387	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12439375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440951	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441084	0.85[AMR][1000 genomes]
rs12443420	0.83[ASN][1000 genomes]
rs12592955	0.82[AMR][1000 genomes]
rs12594667	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594844	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12594938	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16957293	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012253	0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2278543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2415166	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28398258	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28502551	0.82[AMR][1000 genomes]
rs3179616	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34337823	0.82[AMR][1000 genomes]
rs35136341	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3759870	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3850988	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4776611	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs4776616	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777528	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs4777529	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes]
rs4777530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4777531	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4777533	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4777537	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777538	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4777545	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56915357	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57621041	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58600393	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59049627	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59152128	0.82[AMR][1000 genomes]
rs60405894	0.81[AMR][1000 genomes]
rs60601886	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60674997	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61311866	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61632994	0.83[ASN][1000 genomes]
rs62017593	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62017598	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62017623	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72662112	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72737337	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs730180	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs7495022	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7497429	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8032586	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033644	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4777540	ADPGK	cis	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73076800-73078600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:73077000-73078400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr15:73077000-73078400	Enhancers	Fetal Muscle Trunk	muscle
4	chr15:73077000-73078600	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:73077000-73078600	Enhancers	NH-A	brain
6	chr15:73077000-73078800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:73077000-73079000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:73077000-73080600	Enhancers	HSMMtube	muscle
11	chr15:73077000-73088800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:73077200-73078400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:73077200-73078400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:73077200-73078400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:73077200-73078600	Enhancers	NHDF-Ad	bronchial
16	chr15:73077200-73078600	Enhancers	Osteobl	bone
17	chr15:73077200-73078800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:73077200-73079000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:73077200-73079200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr15:73077200-73079200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr15:73077200-73079400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr15:73077200-73079400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:73077200-73079400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:73077200-73079600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:73077200-73079800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:73077200-73079800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:73077200-73079800	Enhancers	Brain Substantia Nigra	brain
28	chr15:73077200-73080000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:73077200-73080000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr15:73077200-73080000	Enhancers	GM12878-XiMat	blood
31	chr15:73077200-73080200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:73077200-73080400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:73077200-73080600	Enhancers	Brain Hippocampus Middle	brain
34	chr15:73077200-73081200	Enhancers	Fetal Brain Male	brain
35	chr15:73077400-73078400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr15:73077400-73078600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:73077400-73078800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:73077400-73079000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:73077400-73079200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:73077400-73079200	Enhancers	Fetal Lung	lung
41	chr15:73077400-73079600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:73077400-73079600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:73077400-73081400	Weak transcription	Spleen	Spleen
44	chr15:73077600-73078600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:73077600-73078800	Enhancers	HepG2	liver
46	chr15:73077600-73080000	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:73077800-73079400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:73077800-73080600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:73078000-73078600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:73078000-73079000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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