Variant report

Variant	rs28525003
Chromosome Location	chr4:667398-667399
allele	C/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	POLR2A	chr4:667278-667468	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:667013-669535	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:667123-668625	K562	blood:	n/a	n/a
4	MXI1	chr4:666896-667855	IMR90	lung:	n/a	n/a
5	POLR2A	chr4:667363-667855	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:667072-669901	HepG2	liver:	n/a	n/a
7	ELK1	chr4:667391-667466	K562	blood:	n/a	n/a
8	POLR2A	chr4:667025-668561	K562	blood:	n/a	n/a
9	SIN3A	chr4:667082-667701	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:667196-667768	SK-N-MC	brain:	n/a	n/a
11	E2F6	chr4:667026-667620	A549	lung:	n/a	chr4:667299-667310
12	POLR2A	chr4:667192-667695	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr4:667036-669605	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr4:667078-668479	H1-hESC	embryonic stem cell:	n/a	n/a
15	CBX3	chr4:666973-667488	K562	blood:	n/a	n/a
16	MYC	chr4:667295-667455	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr4:667118-669869	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:667394-667762	HCT-116	colon:	n/a	n/a
19	POLR2A	chr4:667140-667467	K562	blood:	n/a	n/a
20	POLR2A	chr4:666971-670146	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr4:667057-669372	A549	lung:	n/a	chr4:668220-668229 chr4:668315-668325 chr4:668222-668238
22	MAX	chr4:667020-669306	K562	blood:	n/a	chr4:668220-668229 chr4:668315-668325 chr4:668222-668238
23	POU2F2	chr4:667052-667532	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:667184-669475	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr4:667145-667797	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:667259-667598	HepG2	liver:	n/a	n/a
27	MAX	chr4:667078-667915	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr4:667219-667816	GM12878	blood:	n/a	n/a
29	E2F6	chr4:667143-667835	K562	blood:	n/a	chr4:667299-667310
30	RCOR1	chr4:667324-667471	HepG2	liver:	n/a	n/a
31	POLR2A	chr4:667196-667541	HepG2	liver:	n/a	n/a
32	CREB1	chr4:667033-669390	HepG2	liver:	n/a	chr4:668213-668226
33	ZBTB7A	chr4:667311-667488	HepG2	liver:	n/a	n/a
34	POLR2A	chr4:667196-667631	H1-hESC	embryonic stem cell:	n/a	n/a
35	TBP	chr4:667215-668608	K562	blood:	n/a	n/a
36	MYC	chr4:667364-668388	K562	blood:	n/a	chr4:668220-668229 chr4:668315-668325 chr4:668222-668238
37	TBP	chr4:667201-667531	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr4:667103-667508	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAZ	chr4:667300-669131	K562	blood:	n/a	chr4:668220-668229 chr4:668315-668325 chr4:668222-668238
40	POLR2A	chr4:667149-669626	K562	blood:	n/a	n/a
41	POLR2A	chr4:667230-667580	HepG2	liver:	n/a	n/a
42	E2F6	chr4:667063-667535	K562	blood:	n/a	chr4:667299-667310
43	POLR2A	chr4:666866-675998	K562	blood:	n/a	n/a
44	MYC	chr4:667396-669187	K562	blood:	n/a	chr4:668220-668229 chr4:668315-668325 chr4:668222-668238
45	E2F6	chr4:667031-667600	H1-hESC	embryonic stem cell:	n/a	chr4:667299-667310
46	POLR2A	chr4:667311-672325	GM19193	blood:	n/a	n/a
47	CHD1	chr4:667224-667574	GM12878	blood:	n/a	n/a
48	TBP	chr4:667200-667570	HepG2	liver:	n/a	n/a
49	POLR2A	chr4:667296-675255	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr4:667145-667412	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:666295..671517-chr4:698228..703248,8	MCF-7	breast:
2	chr4:666044..670200-chr4:772961..777371,6	K562	blood:
3	chr4:666011..668174-chr4:698640..701171,3	K562	blood:
4	chr4:665676..669905-chr4:679525..682855,5	K562	blood:
5	chr4:666292..671732-chr4:694079..701503,8	MCF-7	breast:
6	chr17:62831703..62834529-chr4:666982..669061,2	MCF-7	breast:
7	chr4:665710..668196-chr4:979815..981337,2	MCF-7	breast:
8	chr4:665677..668201-chr4:979135..981223,2	K562	blood:

Variant related genes	Relation type
MYL5	TF binding region
ATP5I	TF binding region
ENSG00000249592	Chromatin interaction
ENSG00000169026	Chromatin interaction
ENSG00000214176	Chromatin interaction
ENSG00000145214	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000127415	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10027549	1.00[ASN][1000 genomes]
rs10030136	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs28470912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28568555	1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	1.00[ASN][1000 genomes]
rs28630797	1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	1.00[ASN][1000 genomes]
rs3864130	1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	1.00[ASN][1000 genomes]
rs4463020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518182	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227539	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60316402	1.00[ASN][1000 genomes]
rs71602496	1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985747	0.81[EUR][1000 genomes]
rs9991613	1.00[ASN][1000 genomes]
rs9992641	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv10413	chr4:667204-684301	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28525003	RP11-1191J2.2	cis	Thyroid	GTEx
rs28525003	RP11-1191J2.2	cis	lung	GTEx
rs28525003	RP11-1191J2.2	cis	Nerve Tibial	GTEx
rs28525003	MFSD7	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:658000-667400	Weak transcription	Aorta	Aorta
2	chr4:666600-667400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:666800-667400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
4	chr4:666800-667400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:666800-667400	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
6	chr4:666800-667400	Flanking Active TSS	Fetal Intestine Large	intestine
7	chr4:666800-668800	Active TSS	GM12878-XiMat	blood
8	chr4:667000-667400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:667000-667400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
10	chr4:667000-667400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:667000-667400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:667000-667400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:667000-667400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:667000-667400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:667000-667400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:667000-667400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:667000-667400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:667000-667400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:667000-667400	Flanking Active TSS	Fetal Heart	heart
20	chr4:667000-667400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
21	chr4:667000-667400	Flanking Active TSS	Fetal Kidney	kidney
22	chr4:667000-667400	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
23	chr4:667000-667400	Genic enhancers	Spleen	Spleen
24	chr4:667000-667400	Flanking Active TSS	HSMM	muscle
25	chr4:667000-667400	Transcr. at gene 5' and 3'	K562	blood
26	chr4:667000-667400	Flanking Active TSS	NHDF-Ad	bronchial
27	chr4:667000-667600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:667000-667600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:667000-667600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:667000-667600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:667000-667600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:667000-667600	Flanking Active TSS	Liver	Liver
33	chr4:667000-667600	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr4:667000-667600	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr4:667000-667600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr4:667000-667600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr4:667000-667600	Flanking Active TSS	Fetal Brain Male	brain
38	chr4:667000-667600	Flanking Active TSS	Left Ventricle	heart
39	chr4:667000-667600	Flanking Active TSS	Lung	lung
40	chr4:667000-667600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr4:667000-667600	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr4:667000-667600	Flanking Active TSS	Right Ventricle	heart
43	chr4:667000-667600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr4:667000-667600	Flanking Active TSS	Hela-S3	cervix
45	chr4:667000-667800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr4:667000-667800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr4:667000-667800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr4:667000-667800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:667000-667800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:667000-667800	Flanking Active TSS	Adipose Nuclei	Adipose

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