Variant report

Variant	rs324725
Chromosome Location	chr4:76722579-76722580
allele	G/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	CEBPB	chr4:76722463-76722647	A549	lung:	n/a	n/a

Variant related genes	Relation type
USO1	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10009902	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10010519	0.80[EUR][1000 genomes]
rs10014281	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10025315	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10028884	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10029110	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11097070	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11729258	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11736474	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[EUR][1000 genomes]
rs13116639	0.82[EUR][1000 genomes]
rs13118426	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13119659	0.93[ASN][1000 genomes]
rs13137468	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13138717	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1546539	0.82[EUR][1000 genomes]
rs1548175	0.82[EUR][1000 genomes]
rs1553984	1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs1553986	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs186562	0.81[EUR][1000 genomes]
rs1967495	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1967496	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs226416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280095	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2869174	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs324682	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324683	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324685	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324707	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324715	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324724	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324737	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34385808	0.86[EUR][1000 genomes]
rs3796473	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[EUR][1000 genomes]
rs3796485	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3853183	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes]
rs3853184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3942252	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4349625	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs436611	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs443952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859403	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859543	0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs4859544	0.80[AMR][1000 genomes]
rs4859545	0.82[AMR][1000 genomes]
rs4859546	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859547	0.91[CHD][hapmap];0.81[GIH][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859548	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859550	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5020591	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419115	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531841	0.82[EUR][1000 genomes]
rs6531866	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6531867	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6531868	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6531889	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531902	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531903	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67474106	0.84[EUR][1000 genomes]
rs6826858	0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6827809	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6835702	0.82[EUR][1000 genomes]
rs6835819	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6842216	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855321	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855960	0.84[EUR][1000 genomes]
rs72651313	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7356270	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7356310	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7657871	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7659408	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7662940	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672378	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7674063	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7674328	0.81[TSI][hapmap]
rs7677150	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691385	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691765	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7696241	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7698393	0.89[EUR][1000 genomes]
rs9942164	0.80[AMR][1000 genomes]

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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs324725	PPEF2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
3	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
4	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
6	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:76689400-76724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:76698000-76735400	Weak transcription	Small Intestine	intestine
12	chr4:76698800-76725000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:76699000-76725400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:76699200-76724000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:76699400-76722600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:76701200-76725200	Weak transcription	Thymus	Thymus
17	chr4:76703400-76722800	Weak transcription	Psoas Muscle	Psoas
18	chr4:76704800-76725200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:76705000-76730800	Weak transcription	Fetal Heart	heart
20	chr4:76705800-76725200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:76705800-76730600	Weak transcription	Fetal Brain Female	brain
22	chr4:76706000-76722800	Weak transcription	Ovary	ovary
23	chr4:76706000-76730600	Weak transcription	Aorta	Aorta
24	chr4:76706000-76732000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:76706000-76732000	Weak transcription	Gastric	stomach
26	chr4:76706200-76725000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:76707800-76738600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:76708400-76725200	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:76708400-76735400	Weak transcription	Right Ventricle	heart
30	chr4:76710800-76729400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:76711800-76729400	Weak transcription	Fetal Brain Male	brain
32	chr4:76711800-76729400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:76712200-76729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:76712200-76730600	Weak transcription	Brain Angular Gyrus	brain
35	chr4:76712400-76725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:76712400-76729200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:76712600-76730600	Weak transcription	Brain Germinal Matrix	brain
38	chr4:76712600-76735600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:76713800-76730800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:76715000-76724200	Weak transcription	Fetal Stomach	stomach
41	chr4:76715000-76725200	Weak transcription	Lung	lung
42	chr4:76715000-76725200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:76715000-76730800	Weak transcription	Pancreas	Pancrea
44	chr4:76715000-76734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:76715000-76734600	Weak transcription	Esophagus	oesophagus
46	chr4:76715400-76725200	Weak transcription	HepG2	liver
47	chr4:76715800-76725200	Weak transcription	Primary T cells from cord blood	blood
48	chr4:76716000-76737000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:76716400-76725000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:76716800-76725200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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