Variant report

Variant	rs13142380
Chromosome Location	chr4:87929485-87929486
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	chr4:87929393..87932319-chr4:87992706..87994245,2	K562	blood:
2	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
3	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
4	chr4:87928676..87930653-chr4:88070538..88073339,2	K562	blood:
5	chr4:87929301..87933851-chr4:88000404..88005339,4	K562	blood:
6	chr4:87862443..87864681-chr4:87929416..87931168,2	MCF-7	breast:
7	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:
8	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10029698	0.88[CEU][hapmap];0.87[GIH][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap]
rs1075989	0.88[CEU][hapmap]
rs13105620	1.00[AFR][1000 genomes]
rs13112444	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs13143182	1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[AFR][1000 genomes]
rs13147739	0.82[TSI][hapmap]
rs17704256	0.85[GIH][hapmap];1.00[LWK][hapmap]
rs28458234	0.88[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs28621526	1.00[AFR][1000 genomes]
rs34077745	0.95[EUR][1000 genomes]
rs35534149	1.00[AFR][1000 genomes]
rs35542725	1.00[AFR][1000 genomes]
rs36123985	1.00[AFR][1000 genomes]
rs71605701	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71605702	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71607407	1.00[AFR][1000 genomes]
rs9999554	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13142380	PTPN13	cis	cerebellum	SCAN
rs13142380	PIGY	cis	cerebellum	SCAN
rs13142380	PPM1K	cis	cerebellum	SCAN
rs13142380	PTPN13	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87926800-87929800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:87926800-87930000	Active TSS	Psoas Muscle	Psoas
3	chr4:87926800-87930200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr4:87927000-87929600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:87927000-87929600	Active TSS	Aorta	Aorta
6	chr4:87927000-87930200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr4:87927000-87930200	Active TSS	Thymus	Thymus
8	chr4:87927000-87930400	Active TSS	Colonic Mucosa	Colon
9	chr4:87927000-87930400	Active TSS	Right Ventricle	heart
10	chr4:87927200-87929600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:87927200-87929600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:87927200-87929600	Active TSS	Fetal Stomach	stomach
13	chr4:87927200-87929800	Active TSS	NHDF-Ad	bronchial
14	chr4:87927200-87930000	Active TSS	Rectal Smooth Muscle	rectum
15	chr4:87927200-87930200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:87927200-87930200	Active TSS	Colon Smooth Muscle	Colon
17	chr4:87927200-87930200	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:87927200-87930400	Active TSS	Ovary	ovary
19	chr4:87927400-87929600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr4:87927400-87929600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr4:87927400-87929600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:87927400-87929600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:87927400-87929600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:87927400-87929600	Active TSS	Primary T cells fromperipheralblood	blood
25	chr4:87927400-87929600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr4:87927400-87929600	Active TSS	Fetal Heart	heart
27	chr4:87927400-87929600	Active TSS	Fetal Intestine Small	intestine
28	chr4:87927400-87929600	Active TSS	Left Ventricle	heart
29	chr4:87927400-87930000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:87927400-87930000	Active TSS	Fetal Intestine Large	intestine
31	chr4:87927400-87930200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:87927400-87930200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:87927400-87930200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:87927400-87930400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:87927400-87930400	Active TSS	NHLF	lung
36	chr4:87927600-87929800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:87927600-87929800	Active TSS	Fetal Muscle Leg	muscle
38	chr4:87927600-87930000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:87927600-87930000	Active TSS	Brain Anterior Caudate	brain
40	chr4:87927600-87930000	Active TSS	Fetal Thymus	thymus
41	chr4:87927600-87930200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr4:87927600-87930200	Active TSS	Fetal Kidney	kidney
43	chr4:87927600-87930200	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr4:87927600-87930200	Active TSS	K562	blood
45	chr4:87927600-87932200	Active TSS	GM12878-XiMat	blood
46	chr4:87928600-87930400	Active TSS	Right Atrium	heart
47	chr4:87928600-87931200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr4:87928800-87929600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr4:87928800-87929600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr4:87928800-87929800	Flanking Active TSS	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links