Variant report

Variant	rs4075224
Chromosome Location	chr5:166722486-166722487
allele	A/C
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	chr5:166721784-166723084	A549	lung:	n/a	chr5:166721951-166721963 chr5:166722349-166722360
2	STAT3	chr5:166721829-166723052	MCF10A-Er-Src	breast:	n/a	chr5:166722585-166722594 chr5:166722569-166722581 chr5:166722586-166722595
3	GATA2	chr5:166721807-166722955	HUVEC	blood vessel:	n/a	chr5:166722110-166722119 chr5:166722027-166722036
4	JUND	chr5:166721527-166723382	Hela-S3	cervix:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
5	EP300	chr5:166722470-166722901	SK-N-SH_RA	brain:	n/a	n/a
6	JUND	chr5:166721538-166723027	SK-N-SH	brain:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
7	STAT3	chr5:166721866-166722511	MCF10A-Er-Src	breast:	n/a	n/a
8	FOSL2	chr5:166721832-166722947	A549	lung:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
9	STAT3	chr5:166721499-166722876	Hela-S3	cervix:	n/a	chr5:166722585-166722594 chr5:166722569-166722581 chr5:166722586-166722595
10	FOSL2	chr5:166721826-166722848	SK-N-SH	brain:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
11	GATA3	chr5:166721598-166723147	A549	lung:	n/a	chr5:166722110-166722119 chr5:166722027-166722036
12	USF2	chr5:166721882-166722819	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr5:166722342-166722757	MCF-7	breast:	n/a	n/a
14	GATA3	chr5:166722300-166722875	MCF-7	breast:	n/a	n/a
15	BRCA1	chr5:166721778-166722989	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr5:166721806-166722810	MCF10A-Er-Src	breast:	n/a	chr5:166722585-166722594 chr5:166722569-166722581 chr5:166722586-166722595
17	SP1	chr5:166721783-166722846	A549	lung:	n/a	chr5:166722573-166722583 chr5:166722573-166722583
18	MYC	chr5:166721796-166722909	Hela-S3	cervix:	n/a	chr5:166722349-166722358
19	JUND	chr5:166721705-166722931	SK-N-SH	brain:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
20	RCOR1	chr5:166721366-166722954	Hela-S3	cervix:	n/a	n/a
21	JUND	chr5:166721698-166722917	SK-N-SH	brain:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
22	FOS	chr5:166721784-166722896	MCF10A-Er-Src	breast:	n/a	chr5:166722027-166722038 chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
23	FOS	chr5:166721611-166722959	MCF10A-Er-Src	breast:	n/a	chr5:166722027-166722038 chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
24	EP300	chr5:166721736-166722943	SK-N-SH	brain:	n/a	chr5:166722325-166722339 chr5:166722346-166722360
25	MAFK	chr5:166721765-166722986	Hela-S3	cervix:	n/a	chr5:166722583-166722597 chr5:166722584-166722593 chr5:166722582-166722598 chr5:166722030-166722039 chr5:166722587-166722596 chr5:166722029-166722039
26	TAF1	chr5:166722438-166722629	Hela-S3	cervix:	n/a	n/a
27	MYC	chr5:166721803-166722882	MCF10A-Er-Src	breast:	n/a	chr5:166722349-166722358
28	SIN3AK20	chr5:166721849-166722540	A549	lung:	n/a	n/a
29	STAT1	chr5:166721550-166722903	Hela-S3	cervix:	n/a	chr5:166722585-166722594 chr5:166722569-166722581 chr5:166722586-166722595
30	FOSL2	chr5:166721685-166722939	SK-N-SH	brain:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
31	KAP1	chr5:166721845-166722647	U2OS	brain:	n/a	n/a
32	CEBPB	chr5:166721769-166722953	IMR90	lung:	n/a	chr5:166721951-166721963 chr5:166722349-166722360
33	FOSL2	chr5:166721608-166723052	A549	lung:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
34	FOS	chr5:166721431-166722843	HUVEC	blood vessel:	n/a	chr5:166722027-166722038 chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
35	MYC	chr5:166721792-166723027	MCF10A-Er-Src	breast:	n/a	chr5:166722349-166722358
36	RFX5	chr5:166721720-166722985	Hela-S3	cervix:	n/a	n/a
37	MAX	chr5:166721763-166722863	Hela-S3	cervix:	n/a	chr5:166722349-166722358
38	SMARCC1	chr5:166721418-166723281	Hela-S3	cervix:	n/a	chr5:166722028-166722037
39	FOS	chr5:166721777-166722961	MCF10A-Er-Src	breast:	n/a	chr5:166722027-166722038 chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
40	MAX	chr5:166721766-166722980	Hela-S3	cervix:	n/a	chr5:166722349-166722358
41	EP300	chr5:166721677-166722775	A549	lung:	n/a	chr5:166722325-166722339 chr5:166722346-166722360
42	TCF12	chr5:166721575-166722959	A549	lung:	n/a	n/a
43	POLR2A	chr5:166722330-166722695	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr5:166721721-166723014	Hela-S3	cervix:	n/a	chr5:166721951-166721963 chr5:166722349-166722360
45	GATA2	chr5:166722382-166722840	SH-SY5Y	brain:	n/a	n/a
46	JUND	chr5:166721993-166722503	HepG2	liver:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
47	PBX3	chr5:166721798-166723095	SK-N-SH	brain:	n/a	n/a
48	EP300	chr5:166721731-166722840	A549	lung:	n/a	chr5:166722325-166722339 chr5:166722346-166722360
49	JUND	chr5:166721832-166722791	A549	lung:	n/a	chr5:166722028-166722038 chr5:166722109-166722117 chr5:166722027-166722039 chr5:166722018-166722030 chr5:166722028-166722038 chr5:166722029-166722037 chr5:166722028-166722038 chr5:166722107-166722119
50	CEBPB	chr5:166721947-166722941	A549	lung:	n/a	chr5:166721951-166721963 chr5:166722349-166722360

Variant related genes	Relation type
ENSG00000254365	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10043619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10462891	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475839	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739327	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13355217	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4349736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56857681	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59094139	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61241624	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6865179	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7341056	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7730469	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7731005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[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	nsv869374	chr5:166488702-166817411	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1032183	chr5:166612188-166732287	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv883100	chr5:166718807-166808602	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4075224	LOC257358	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:166720400-166724000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:166720600-166724000	Enhancers	Fetal Lung	lung
3	chr5:166720800-166724600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:166720800-166724600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:166720800-166724800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:166721000-166722600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr5:166721000-166723000	Enhancers	Ovary	ovary
8	chr5:166721000-166724400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:166721000-166724600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:166721000-166724600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr5:166721200-166723000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:166721200-166723800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:166721400-166723000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr5:166721400-166723200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:166721400-166724000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:166721400-166724000	Enhancers	HSMM	muscle
17	chr5:166721400-166724000	Enhancers	HSMMtube	muscle
18	chr5:166721400-166724600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:166721600-166722600	Enhancers	Fetal Stomach	stomach
20	chr5:166721600-166724600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr5:166721800-166723800	Enhancers	Adipose Nuclei	Adipose
22	chr5:166721800-166724000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr5:166721800-166724000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr5:166721800-166724000	Enhancers	Brain Hippocampus Middle	brain
25	chr5:166722000-166722600	Enhancers	Brain Germinal Matrix	brain
26	chr5:166722000-166722600	Enhancers	Colon Smooth Muscle	Colon
27	chr5:166722000-166722600	Active TSS	A549	lung
28	chr5:166722000-166722800	Flanking Active TSS	NHEK	skin
29	chr5:166722000-166723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:166722000-166723000	Enhancers	Brain Angular Gyrus	brain
31	chr5:166722000-166723000	Enhancers	Duodenum Mucosa	Duodenum
32	chr5:166722000-166723200	Weak transcription	Small Intestine	intestine
33	chr5:166722000-166723800	Flanking Active TSS	Hela-S3	cervix
34	chr5:166722200-166722600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
35	chr5:166722200-166722600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:166722200-166722600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr5:166722200-166722600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:166722200-166722600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:166722200-166722600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:166722200-166722600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:166722200-166722600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:166722200-166722600	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:166722200-166722600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr5:166722200-166722600	Flanking Active TSS	HMEC	breast
45	chr5:166722200-166722600	Flanking Active TSS	HUVEC	blood vessel
46	chr5:166722200-166722600	Flanking Active TSS	NHLF	lung
47	chr5:166722200-166722600	Flanking Active TSS	Osteobl	bone
48	chr5:166722200-166722800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:166722200-166722800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:166722200-166722800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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