Variant report

Variant	rs2875040
Chromosome Location	chr4:22482353-22482354
allele	A/G
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	NFYA	chr4:22482297-22482701	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
GPR125	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1020917	0.81[CHB][hapmap]
rs1026659	0.97[ASN][1000 genomes]
rs10938901	0.95[ASN][1000 genomes]
rs11730179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933465	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.98[ASN][1000 genomes]
rs12646648	0.97[ASN][1000 genomes]
rs13101873	0.88[ASN][1000 genomes]
rs13109271	0.97[ASN][1000 genomes]
rs13125682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13136131	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs13150142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564138	0.81[CHB][hapmap]
rs1564139	0.81[CHB][hapmap]
rs16872728	0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2323412	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4697307	0.84[JPT][hapmap]
rs56235800	0.83[ASN][1000 genomes]
rs61792059	0.92[ASN][1000 genomes]
rs7673893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7697601	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7697959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs9790453	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2875040	PPARGC1A	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
2	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:22456800-22485000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:22462000-22493200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:22462400-22483600	Weak transcription	Liver	Liver
7	chr4:22466600-22484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:22472600-22484200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:22472600-22484400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:22472600-22486200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:22472800-22482400	Weak transcription	Ovary	ovary
12	chr4:22473000-22482400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:22473200-22487400	Weak transcription	Right Ventricle	heart
14	chr4:22473400-22484400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:22473600-22484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:22474000-22483200	Weak transcription	Fetal Brain Female	brain
17	chr4:22474200-22484000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:22474200-22486200	Weak transcription	Fetal Stomach	stomach
19	chr4:22474400-22484200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:22474400-22484400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:22474600-22482400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:22474600-22484200	Weak transcription	HSMMtube	muscle
23	chr4:22475000-22484000	Weak transcription	Left Ventricle	heart
24	chr4:22475000-22484800	Weak transcription	Fetal Intestine Large	intestine
25	chr4:22475000-22489400	Weak transcription	Lung	lung
26	chr4:22475200-22482400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:22475200-22484200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:22475200-22486000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:22476600-22482600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:22476600-22484400	Weak transcription	Psoas Muscle	Psoas
31	chr4:22476600-22485200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:22476600-22487200	Weak transcription	Small Intestine	intestine
33	chr4:22477000-22482400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:22477000-22482400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:22477000-22482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:22477000-22482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:22477000-22484600	Weak transcription	Hela-S3	cervix
38	chr4:22477000-22484800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:22477000-22485000	Weak transcription	A549	lung
40	chr4:22477200-22482400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:22477200-22484400	Weak transcription	Pancreas	Pancrea
42	chr4:22477600-22482400	Weak transcription	NHEK	skin
43	chr4:22477800-22482400	Weak transcription	Fetal Heart	heart
44	chr4:22477800-22489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:22478000-22482400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:22478000-22484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:22478000-22484600	Weak transcription	HepG2	liver
48	chr4:22478200-22482600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:22479400-22484600	Weak transcription	Fetal Lung	lung
50	chr4:22479600-22485000	Weak transcription	Colon Smooth Muscle	Colon

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