Variant report

Variant	rs59231873
Chromosome Location	chr4:528481-528482
allele	C/T
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	chr4:527861-529061	K562	blood:	n/a	n/a
2	CTCF	chr4:528400-528550	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:527516..530204-chr4:530528..533344,2	MCF-7	breast:
2	chr4:526650..530036-chr4:530929..534159,4	K562	blood:

Variant related genes	Relation type
PIGG	TF binding region
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10003485	0.96[ASN][1000 genomes]
rs10006279	0.91[ASN][1000 genomes]
rs10014602	0.96[ASN][1000 genomes]
rs10014828	0.93[ASN][1000 genomes]
rs10015083	0.93[ASN][1000 genomes]
rs10022506	0.93[ASN][1000 genomes]
rs10026805	0.92[ASN][1000 genomes]
rs10027093	0.92[ASN][1000 genomes]
rs10027174	0.93[ASN][1000 genomes]
rs10213007	0.86[ASN][1000 genomes]
rs10213020	0.96[ASN][1000 genomes]
rs11248023	0.96[ASN][1000 genomes]
rs1127410	0.96[ASN][1000 genomes]
rs11730410	0.93[ASN][1000 genomes]
rs11931500	0.94[ASN][1000 genomes]
rs11931543	0.96[ASN][1000 genomes]
rs11931692	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11933478	0.94[ASN][1000 genomes]
rs11934533	0.96[ASN][1000 genomes]
rs11934538	0.96[ASN][1000 genomes]
rs11934549	0.94[ASN][1000 genomes]
rs11936515	0.96[ASN][1000 genomes]
rs11936548	0.96[ASN][1000 genomes]
rs11936717	0.96[ASN][1000 genomes]
rs11936752	0.90[ASN][1000 genomes]
rs11938183	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11938226	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11940796	0.96[ASN][1000 genomes]
rs11940914	0.96[ASN][1000 genomes]
rs11944995	0.92[ASN][1000 genomes]
rs11946204	0.94[ASN][1000 genomes]
rs13105387	0.95[ASN][1000 genomes]
rs13106068	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13110171	0.94[ASN][1000 genomes]
rs13111014	0.93[ASN][1000 genomes]
rs13115802	0.93[ASN][1000 genomes]
rs13119658	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13137203	0.93[ASN][1000 genomes]
rs13141560	0.96[ASN][1000 genomes]
rs13149933	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28380061	0.92[ASN][1000 genomes]
rs28407137	0.93[ASN][1000 genomes]
rs28458903	0.92[ASN][1000 genomes]
rs28465192	0.93[ASN][1000 genomes]
rs28465521	0.93[ASN][1000 genomes]
rs28473153	0.85[ASN][1000 genomes]
rs28491533	0.93[ASN][1000 genomes]
rs28535797	0.93[ASN][1000 genomes]
rs28549216	0.93[ASN][1000 genomes]
rs28624264	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28652818	0.93[ASN][1000 genomes]
rs28673088	0.93[ASN][1000 genomes]
rs28684815	0.96[ASN][1000 genomes]
rs28715137	0.92[ASN][1000 genomes]
rs3211083	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34247702	0.96[ASN][1000 genomes]
rs34327839	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34584074	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34623004	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs35122538	0.93[ASN][1000 genomes]
rs35479345	0.96[ASN][1000 genomes]
rs35629431	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs36043622	0.95[ASN][1000 genomes]
rs4324509	0.93[ASN][1000 genomes]
rs4324510	0.93[ASN][1000 genomes]
rs4356866	0.93[ASN][1000 genomes]
rs4488886	0.93[ASN][1000 genomes]
rs55983970	0.96[ASN][1000 genomes]
rs56121355	0.95[ASN][1000 genomes]
rs59564702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61334630	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6816690	0.93[ASN][1000 genomes]
rs6817963	0.93[ASN][1000 genomes]
rs6817973	0.93[ASN][1000 genomes]
rs6822767	0.93[ASN][1000 genomes]
rs6827438	0.93[ASN][1000 genomes]
rs6833031	0.93[ASN][1000 genomes]
rs6837492	0.93[ASN][1000 genomes]
rs6847050	0.93[ASN][1000 genomes]
rs6847066	0.93[ASN][1000 genomes]
rs6852371	0.93[ASN][1000 genomes]
rs6855585	0.93[ASN][1000 genomes]
rs72501954	0.95[ASN][1000 genomes]
rs73072173	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73072175	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73072198	0.93[ASN][1000 genomes]
rs73792305	0.93[ASN][1000 genomes]
rs73792306	0.93[ASN][1000 genomes]
rs73794942	0.90[ASN][1000 genomes]
rs7441980	0.92[ASN][1000 genomes]
rs7668455	0.96[ASN][1000 genomes]
rs9884673	0.93[ASN][1000 genomes]
rs9884677	0.93[ASN][1000 genomes]
rs9884771	0.93[ASN][1000 genomes]
rs9884772	0.93[ASN][1000 genomes]
rs9884826	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	esv3357582	chr4:526002-528800	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:494400-531000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:494400-533200	Strong transcription	Placenta	Placenta
3	chr4:494400-534600	Weak transcription	Fetal Heart	heart
4	chr4:494600-532000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:494600-533000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:494600-533200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:494600-533200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:495000-533000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:495200-533000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:495200-534000	Strong transcription	Fetal Stomach	stomach
11	chr4:496400-533000	Strong transcription	Fetal Brain Female	brain
12	chr4:496800-532000	Strong transcription	Dnd41	blood
13	chr4:503000-530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:503000-531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:503200-530800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr4:503600-532000	Strong transcription	Primary T cells from cord blood	blood
17	chr4:503800-532800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:506400-533200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:506600-531800	Strong transcription	Thymus	Thymus
20	chr4:506600-532200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:506600-532800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:506600-533200	Strong transcription	Fetal Intestine Large	intestine
23	chr4:506600-533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:506600-533600	Strong transcription	Liver	Liver
25	chr4:506800-532000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:506800-532600	Strong transcription	Aorta	Aorta
27	chr4:506800-533000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr4:506800-533200	Strong transcription	Fetal Muscle Leg	muscle
29	chr4:507200-533400	Strong transcription	Brain Anterior Caudate	brain
30	chr4:507400-533600	Strong transcription	Brain Hippocampus Middle	brain
31	chr4:507600-533200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:507600-533600	Strong transcription	Brain Cingulate Gyrus	brain
33	chr4:508600-532000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:508600-532200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:508600-532800	Strong transcription	Fetal Intestine Small	intestine
36	chr4:509000-529600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:509200-530600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:510000-535400	Weak transcription	Hela-S3	cervix
39	chr4:510400-531800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:513400-533000	Strong transcription	Gastric	stomach
41	chr4:514000-530800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:514000-532000	Strong transcription	Right Ventricle	heart
43	chr4:514200-532000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:514200-532200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:514400-528600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:514400-533200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:514400-533200	Strong transcription	Adipose Nuclei	Adipose
48	chr4:514400-533200	Strong transcription	Left Ventricle	heart
49	chr4:514400-533400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:514600-529800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links