Variant report

Variant	rs13143182
Chromosome Location	chr4:88008401-88008402
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87925271..87927953-chr4:88006288..88008752,2	K562	blood:
2	chr4:88005383..88008853-chr4:88008930..88010972,3	K562	blood:
3	chr4:87925271..87928107-chr4:88005926..88008504,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12710836	1.00[LWK][hapmap];0.84[TSI][hapmap]
rs13105620	1.00[AFR][1000 genomes]
rs13112444	0.82[MKK][hapmap]
rs13134294	1.00[AFR][1000 genomes]
rs13134907	1.00[AFR][1000 genomes]
rs13142380	1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[AFR][1000 genomes]
rs13145898	0.88[AMR][1000 genomes]
rs13435811	1.00[LWK][hapmap];0.85[TSI][hapmap]
rs17704256	1.00[LWK][hapmap];0.86[TSI][hapmap]
rs2054611	0.80[AMR][1000 genomes]
rs28621526	1.00[AFR][1000 genomes]
rs28668976	0.80[AMR][1000 genomes]
rs28773027	0.84[AMR][1000 genomes]
rs34242006	1.00[AFR][1000 genomes]
rs34422965	1.00[AFR][1000 genomes]
rs34589806	1.00[AFR][1000 genomes]
rs35133616	1.00[AFR][1000 genomes]
rs35534149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35542725	1.00[AFR][1000 genomes]
rs36123985	1.00[AFR][1000 genomes]
rs71607405	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71607407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9999554	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13143182	PTPN13	cis	parietal	SCAN
rs13143182	KLHL8	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88009400	Weak transcription	HepG2	liver
2	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
6	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:87999400-88010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:87999600-88010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:87999600-88011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:88000200-88010600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:88000600-88013000	Weak transcription	A549	lung
14	chr4:88001200-88011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:88001400-88013800	Weak transcription	HSMM	muscle
16	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
18	chr4:88001800-88010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:88001800-88011800	Weak transcription	Fetal Stomach	stomach
20	chr4:88001800-88013200	Weak transcription	Stomach Mucosa	stomach
21	chr4:88001800-88013400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:88001800-88013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:88001800-88025200	Weak transcription	Gastric	stomach
24	chr4:88002000-88009800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
26	chr4:88003600-88013000	Weak transcription	HMEC	breast
27	chr4:88003600-88013200	Weak transcription	Osteobl	bone
28	chr4:88004200-88010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:88004800-88009000	Enhancers	Psoas Muscle	Psoas
32	chr4:88004800-88010400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:88005000-88008800	Strong transcription	Primary B cells from cord blood	blood
34	chr4:88005000-88017400	Strong transcription	Dnd41	blood
35	chr4:88005200-88008800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:88005400-88009400	Strong transcription	Primary T cells from cord blood	blood
37	chr4:88005800-88014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:88006000-88008600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr4:88006000-88008800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:88006200-88010600	Weak transcription	NHDF-Ad	bronchial
41	chr4:88006200-88011200	Weak transcription	Fetal Lung	lung
42	chr4:88006400-88010800	Weak transcription	K562	blood
43	chr4:88007000-88008800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:88007000-88009000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:88007000-88010400	Genic enhancers	Left Ventricle	heart
46	chr4:88007200-88009600	Enhancers	Colon Smooth Muscle	Colon
47	chr4:88007400-88009000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr4:88007400-88010000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr4:88007600-88009000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:88007600-88009600	Strong transcription	Hela-S3	cervix

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