Variant report

Variant	rs28586910
Chromosome Location	chr4:656604-656605
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:646849..649113-chr4:654761..657491,3	K562	blood:

Variant related genes	Relation type
ENSG00000133256	Chromatin interaction
ENSG00000242686	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1135375	0.82[EUR][1000 genomes]
rs13119162	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28568555	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28583078	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28630797	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28742899	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3864130	0.88[EUR][1000 genomes]
rs3891250	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60316402	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71602496	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9985747	0.84[AMR][1000 genomes]
rs9992641	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	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
17	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
18	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28586910	RP11-1191J2.2	cis	lung	GTEx
rs28586910	RP11-1191J2.2	cis	Thyroid	GTEx
rs28586910	RP11-1191J2.2	cis	Nerve Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:645800-656800	Weak transcription	Gastric	stomach
6	chr4:648400-657000	Weak transcription	Right Ventricle	heart
7	chr4:651600-657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:651600-657200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:651800-656800	Weak transcription	Primary B cells from cord blood	blood
10	chr4:652000-656800	Weak transcription	Fetal Lung	lung
11	chr4:652400-656800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:652600-656800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:652600-656800	Weak transcription	Fetal Thymus	thymus
14	chr4:653000-656800	Weak transcription	Fetal Heart	heart
15	chr4:653000-657000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:653200-656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:653200-657000	Weak transcription	Fetal Kidney	kidney
18	chr4:653200-657000	Weak transcription	Ovary	ovary
19	chr4:653400-656800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:653600-656800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:653600-656800	Strong transcription	Fetal Stomach	stomach
22	chr4:653600-657000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:653800-656800	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:654000-656800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:654000-656800	Weak transcription	Brain Anterior Caudate	brain
26	chr4:654000-656800	Weak transcription	Fetal Brain Male	brain
27	chr4:654200-657000	Weak transcription	HepG2	liver
28	chr4:654400-656800	Weak transcription	Brain Substantia Nigra	brain
29	chr4:654400-657000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:654600-656800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:654600-656800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:655600-657200	Enhancers	Spleen	Spleen
33	chr4:655800-656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:655800-656800	Weak transcription	Fetal Intestine Small	intestine
35	chr4:656000-656800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:656000-657200	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr4:656200-656800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:656200-656800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr4:656200-656800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr4:656200-656800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr4:656200-656800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:656200-657000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:656200-657000	Enhancers	Lung	lung
44	chr4:656400-656800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:656400-656800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:656400-656800	Enhancers	Pancreas	Pancrea
47	chr4:656400-657200	Enhancers	Esophagus	oesophagus
48	chr4:656600-656800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:656600-656800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr4:656600-656800	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links