Variant report

Variant	rs4579747
Chromosome Location	chr1:154153106-154153107
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	SPI1	chr1:154152552-154153313	GM12878	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019
2	JUN	chr1:154152734-154153174	K562	blood:	n/a	n/a
3	POLR2A	chr1:154152625-154153811	K562	blood:	n/a	n/a
4	POLR2A	chr1:154152523-154153111	GM12878	blood:	n/a	n/a
5	SPI1	chr1:154152848-154153155	GM12878	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019
6	POLR2A	chr1:154152526-154153500	PFSK-1	brain:	n/a	n/a
7	SPI1	chr1:154152782-154153134	HL-60	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019
8	NR2F2	chr1:154152637-154153167	MCF-7	breast:	n/a	n/a
9	SPI1	chr1:154152483-154153187	GM12891	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019
10	SPI1	chr1:154152828-154153149	GM12891	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019
11	SPI1	chr1:154152654-154153167	HL-60	blood:	n/a	chr1:154153008-154153017 chr1:154153007-154153020 chr1:154153006-154153019

No.	Distal block	Cell Line	Cell type
1	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
2	chr1:153962189..153967020-chr1:154149779..154153923,7	MCF-7	breast:
3	chr1:154130046..154131854-chr1:154151201..154154094,2	K562	blood:
4	chr1:154139117..154140929-chr1:154152481..154154257,2	MCF-7	breast:
5	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
6	chr1:154152596..154154922-chr1:154174225..154175746,2	MCF-7	breast:
7	chr1:153961881..153966027-chr1:154151379..154156773,10	MCF-7	breast:
8	chr1:153936098..153938705-chr1:154152746..154155431,3	MCF-7	breast:
9	chr1:153948325..153950818-chr1:154153014..154155918,2	MCF-7	breast:
10	chr1:154151312..154154033-chr1:154243382..154245997,2	K562	blood:
11	chr1:154152910..154155985-chr1:154176488..154179732,3	K562	blood:
12	chr1:153917479..153920688-chr1:154153090..154156398,3	MCF-7	breast:
13	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
14	chr1:153961765..153965852-chr1:154152407..154156955,8	K562	blood:

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000163263	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000272654	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10797058	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10797061	0.82[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10908739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908751	1.00[ASW][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11265285	0.82[EUR][1000 genomes]
rs1194580	1.00[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1194582	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1194599	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1194600	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1194602	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1194603	1.00[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs1194604	0.90[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12044616	0.87[EUR][1000 genomes]
rs12063830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][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]
rs12095767	0.83[EUR][1000 genomes]
rs2220390	0.90[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2790690	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3001363	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4072431	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4364874	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4393149	1.00[ASW][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4400599	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540651	1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs4845609	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845610	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6680947	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7516809	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7521047	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7526644	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7533952	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7537213	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9803862	0.90[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs9804045	1.00[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9943097	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4579747	SF3B4	cis	parietal	SCAN
rs4579747	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs4579747	FLG	cis	parietal	SCAN
rs4579747	SLC27A3	cis	cerebellum	SCAN
rs4579747	CKS1B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154143800-154153600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
2	chr1:154144200-154154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:154145800-154153400	Weak transcription	Fetal Kidney	kidney
4	chr1:154148200-154153800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:154148600-154154400	Enhancers	Brain Angular Gyrus	brain
6	chr1:154148600-154155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:154148800-154153200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:154148800-154154400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:154149000-154153400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:154149200-154153400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:154149400-154154400	Enhancers	Spleen	Spleen
12	chr1:154149600-154153200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:154149600-154153800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr1:154149800-154153200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154149800-154154600	Enhancers	Fetal Heart	heart
16	chr1:154150000-154153200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:154150000-154153600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:154150000-154153600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
19	chr1:154150000-154153800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr1:154150200-154153400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:154150200-154154400	Enhancers	Fetal Brain Male	brain
22	chr1:154150600-154153200	Genic enhancers	Fetal Stomach	stomach
23	chr1:154150600-154153200	Genic enhancers	Lung	lung
24	chr1:154150600-154153200	Enhancers	Ovary	ovary
25	chr1:154150600-154153200	Transcr. at gene 5' and 3'	Hela-S3	cervix
26	chr1:154150800-154153600	Enhancers	Pancreas	Pancrea
27	chr1:154151200-154153400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:154151200-154153400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:154151200-154153400	Genic enhancers	HSMM	muscle
30	chr1:154151200-154154000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:154151200-154154800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr1:154151400-154153200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:154151400-154153600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:154151400-154153800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
35	chr1:154151400-154154000	Enhancers	Small Intestine	intestine
36	chr1:154151400-154154800	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr1:154151600-154154000	Enhancers	Fetal Intestine Large	intestine
38	chr1:154151600-154156400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:154151800-154153200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr1:154151800-154153400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:154151800-154154800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:154152000-154153200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:154152000-154153600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:154152000-154153600	Weak transcription	HSMMtube	muscle
45	chr1:154152000-154153800	Weak transcription	Brain Substantia Nigra	brain
46	chr1:154152000-154153800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr1:154152000-154154000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:154152000-154154400	Weak transcription	Aorta	Aorta
49	chr1:154152000-154155400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr1:154152200-154153400	Genic enhancers	Fetal Intestine Small	intestine

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