Variant report

Variant	rs13053009
Chromosome Location	chr21:46304314-46304315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46299899..46304790-chr21:46308846..46313230,4	K562	blood:
2	chr21:46298053..46300206-chr21:46304270..46306029,2	K562	blood:
3	chr21:46298853..46300793-chr21:46302963..46305695,2	MCF-7	breast:
4	chr21:46236362..46238915-chr21:46304111..46306677,3	MCF-7	breast:
5	chr21:46302796..46304799-chr21:46319469..46322179,2	MCF-7	breast:
6	chr21:46264572..46266878-chr21:46303088..46304857,2	K562	blood:
7	chr21:46292064..46297590-chr21:46299437..46304733,9	MCF-7	breast:
8	chr21:46302013..46304883-chr21:46310101..46313045,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183255	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13050333	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13050968	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117341	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277811	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282114	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34940823	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35207173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35871743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810586	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66467973	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67786546	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238097	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73239703	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv470908	chr21:46298869-46335580	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13053009	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL
rs13053009	PTTG1IP	cis	Artery Aorta	GTEx
rs13053009	PTTG1IP	cis	lung	GTEx
rs13053009	PTTG1IP	cis	Artery Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46295600-46338800	Weak transcription	Right Atrium	heart
2	chr21:46296000-46304600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr21:46296000-46307400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr21:46298400-46326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr21:46300200-46304600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr21:46300400-46310000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr21:46301400-46305400	Weak transcription	Dnd41	blood
8	chr21:46301600-46304600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr21:46301600-46305400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr21:46301800-46304400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr21:46301800-46304600	Enhancers	HepG2	liver
12	chr21:46302000-46305400	Weak transcription	Liver	Liver
13	chr21:46302200-46305400	Weak transcription	Thymus	Thymus
14	chr21:46302200-46308000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:46302200-46309800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr21:46302400-46304400	Weak transcription	Brain Hippocampus Middle	brain
17	chr21:46302400-46305400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr21:46302400-46305400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr21:46302400-46305800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr21:46302400-46306000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr21:46302400-46309600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr21:46302600-46305400	Weak transcription	Primary T cells from cord blood	blood
23	chr21:46302600-46305400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr21:46302600-46305800	Weak transcription	GM12878-XiMat	blood
25	chr21:46302600-46306000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr21:46302600-46306800	Weak transcription	Lung	lung
27	chr21:46302600-46310000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr21:46302800-46304400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr21:46302800-46305400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr21:46302800-46305400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr21:46302800-46305400	Weak transcription	Right Ventricle	heart
32	chr21:46302800-46305600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr21:46302800-46305600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr21:46302800-46306400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:46303000-46305400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr21:46303000-46310800	Weak transcription	Fetal Intestine Small	intestine
37	chr21:46303200-46304400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr21:46303600-46304600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr21:46303600-46305400	Weak transcription	Fetal Thymus	thymus
40	chr21:46303600-46306400	Weak transcription	Primary B cells from cord blood	blood
41	chr21:46303800-46304400	Weak transcription	HMEC	breast
42	chr21:46303800-46306800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr21:46304000-46304600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr21:46304200-46304400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr21:46304200-46304400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr21:46304200-46304400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:46304200-46304400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr21:46304200-46304400	ZNF genes & repeats	Esophagus	oesophagus
49	chr21:46304200-46304400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
50	chr21:46304200-46304600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links