Variant report

Variant	rs4690292
Chromosome Location	chr4:703712-703713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:703233..707351-chr4:710441..713114,3	MCF-7	breast:
2	chr4:701950..703734-chr4:716320..717930,2	K562	blood:
3	chr4:697549..703820-chr4:770860..775722,9	K562	blood:
4	chr4:697170..699923-chr4:703607..707552,5	K562	blood:
5	chr4:671675..674589-chr4:702337..705311,3	MCF-7	breast:
6	chr4:687290..688821-chr4:702192..704645,2	MCF-7	breast:
7	chr4:700678..704217-chr4:710705..714201,3	MCF-7	breast:
8	chr4:702491..704848-chr4:710046..712151,2	K562	blood:

Variant related genes	Relation type
ENSG00000248416	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000215375	Chromatin interaction
ENSG00000249592	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11248035	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11248036	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11734460	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735280	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs11940788	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12374317	0.90[CEU][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12504026	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4690186	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690187	0.90[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4690188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690293	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690294	0.80[ASN][1000 genomes]
rs4690295	0.80[ASN][1000 genomes]
rs73221103	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73221104	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73221124	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4690292	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:700000-704400	Enhancers	Fetal Brain Male	brain
2	chr4:701000-704000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:701000-704000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr4:701000-705800	Weak transcription	Fetal Kidney	kidney
5	chr4:701200-704400	Enhancers	Right Atrium	heart
6	chr4:701200-704600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:701200-713400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:701200-713400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:701200-714600	Weak transcription	NHDF-Ad	bronchial
10	chr4:701200-724400	Weak transcription	Aorta	Aorta
11	chr4:701400-704200	Enhancers	Right Ventricle	heart
12	chr4:701400-705000	Enhancers	Pancreas	Pancrea
13	chr4:701400-705200	Strong transcription	Fetal Intestine Small	intestine
14	chr4:701400-714000	Weak transcription	HMEC	breast
15	chr4:701400-715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:701400-724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:701400-724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:701600-716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:701800-705000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:702000-704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:702000-704000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr4:702000-704400	Genic enhancers	Fetal Muscle Leg	muscle
23	chr4:702000-704400	Enhancers	Small Intestine	intestine
24	chr4:702000-705000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:702000-705000	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr4:702200-705000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:702200-705000	Genic enhancers	Spleen	Spleen
28	chr4:702200-754800	Weak transcription	Hela-S3	cervix
29	chr4:702400-704200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr4:702400-704400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:702400-704800	Enhancers	Brain Hippocampus Middle	brain
32	chr4:702400-705000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:702400-708000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:702400-714600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:702400-720000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:702400-720200	Weak transcription	NH-A	brain
37	chr4:702600-703800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:702600-703800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:702600-704000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:702600-704000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:702600-704000	Enhancers	Adipose Nuclei	Adipose
42	chr4:702600-704000	Weak transcription	Esophagus	oesophagus
43	chr4:702600-704000	Enhancers	Ovary	ovary
44	chr4:702600-704000	Weak transcription	Thymus	Thymus
45	chr4:702600-704200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:702600-704200	Weak transcription	Fetal Intestine Large	intestine
47	chr4:702600-704400	Enhancers	Brain Anterior Caudate	brain
48	chr4:702600-704400	Enhancers	Brain Cingulate Gyrus	brain
49	chr4:702600-704400	Genic enhancers	HepG2	liver
50	chr4:702600-704800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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