Variant report

Variant	rs11933465
Chromosome Location	chr4:22476571-22476572
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	CEBPB	chr4:22476298-22476627	Hela-S3	cervix:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
2	FOXA1	chr4:22476297-22477038	HepG2	liver:	n/a	n/a
3	CEBPB	chr4:22476284-22476644	H1-hESC	embryonic stem cell:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
4	CEBPB	chr4:22476127-22477207	HCT-116	colon:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
5	JUND	chr4:22476382-22476985	HepG2	liver:	n/a	n/a
6	TCF12	chr4:22476485-22477112	SK-N-SH	brain:	n/a	n/a
7	SMC3	chr4:22476286-22476611	HepG2	liver:	n/a	n/a
8	CEBPB	chr4:22476256-22476577	HepG2	liver:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
9	FOSL1	chr4:22476437-22477127	HCT-116	colon:	n/a	n/a
10	POLR2A	chr4:22476392-22476814	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr4:22476553-22476988	MCF10A-Er-Src	breast:	n/a	n/a
12	BHLHE40	chr4:22476315-22476977	HepG2	liver:	n/a	n/a
13	EP300	chr4:22476208-22476597	HepG2	liver:	n/a	chr4:22476453-22476467
14	CEBPB	chr4:22476253-22476646	HepG2	liver:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
15	FOSL1	chr4:22476547-22477114	HCT-116	colon:	n/a	n/a
16	JUN	chr4:22476387-22476915	HepG2	liver:	n/a	n/a
17	JUND	chr4:22476562-22477085	SK-N-SH	brain:	n/a	n/a
18	ARID3A	chr4:22476377-22477117	HepG2	liver:	n/a	n/a
19	POLR2A	chr4:22476378-22476844	MCF10A-Er-Src	breast:	n/a	n/a
20	MYBL2	chr4:22476188-22476932	HepG2	liver:	n/a	n/a
21	TEAD4	chr4:22476224-22476974	HepG2	liver:	n/a	n/a
22	FOXA1	chr4:22476308-22477057	HepG2	liver:	n/a	n/a
23	EP300	chr4:22476208-22476581	HepG2	liver:	n/a	chr4:22476453-22476467
24	JUND	chr4:22476469-22477136	HCT-116	colon:	n/a	n/a
25	CEBPB	chr4:22476270-22476653	HepG2	liver:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
26	CEBPB	chr4:22476288-22477066	IMR90	lung:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
27	SP1	chr4:22476520-22477142	HCT-116	colon:	n/a	n/a
28	CEBPB	chr4:22476204-22477125	HCT-116	colon:	n/a	chr4:22476452-22476465 chr4:22476454-22476465 chr4:22476452-22476463 chr4:22476454-22476465 chr4:22476452-22476465
29	HEY1	chr4:22476329-22476617	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:75007030..75007602-chr4:22476562..22477062,2	Hela-S3	cervix:

Variant related genes	Relation type
GPR125	TF binding region
ENSG00000236756	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1020917	0.81[CHB][hapmap]
rs1026659	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938901	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12646648	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101455	0.81[ASN][1000 genomes]
rs13101873	0.89[ASN][1000 genomes]
rs13109271	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13136131	0.89[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs13150142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs2875040	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]
rs4697307	0.84[JPT][hapmap]
rs56235800	0.83[ASN][1000 genomes]
rs61792059	0.92[ASN][1000 genomes]
rs7673893	0.97[ASN][1000 genomes]
rs7697601	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7697959	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790453	0.98[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
rs11933465	PPARGC1A	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
2	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:22456800-22479000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:22456800-22485000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:22462000-22493200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:22462400-22483600	Weak transcription	Liver	Liver
9	chr4:22462600-22478400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:22466400-22477600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:22466600-22484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:22472200-22480200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:22472600-22477200	Enhancers	HMEC	breast
14	chr4:22472600-22484200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:22472600-22484400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:22472600-22486200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:22472800-22477000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:22472800-22482400	Weak transcription	Ovary	ovary
19	chr4:22473000-22482400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:22473200-22487400	Weak transcription	Right Ventricle	heart
21	chr4:22473400-22484400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:22473600-22476600	Enhancers	Fetal Lung	lung
23	chr4:22473600-22484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:22473800-22477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:22474000-22483200	Weak transcription	Fetal Brain Female	brain
26	chr4:22474200-22477800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:22474200-22484000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:22474200-22486200	Weak transcription	Fetal Stomach	stomach
29	chr4:22474400-22479200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:22474400-22484200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:22474400-22484400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:22474600-22478200	Enhancers	Osteobl	bone
33	chr4:22474600-22482400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:22474600-22484200	Weak transcription	HSMMtube	muscle
35	chr4:22474800-22478000	Enhancers	HUVEC	blood vessel
36	chr4:22474800-22482000	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:22475000-22476600	Enhancers	HSMM	muscle
38	chr4:22475000-22480000	Weak transcription	Primary T cells from cord blood	blood
39	chr4:22475000-22484000	Weak transcription	Left Ventricle	heart
40	chr4:22475000-22484800	Weak transcription	Fetal Intestine Large	intestine
41	chr4:22475000-22489400	Weak transcription	Lung	lung
42	chr4:22475200-22479600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:22475200-22480000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:22475200-22482400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:22475200-22484200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:22475200-22486000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:22475400-22477000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:22475800-22476800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr4:22475800-22477000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:22475800-22477000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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