Variant report

Variant	rs28668976
Chromosome Location	chr4:88082281-88082282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:88080915..88083555-chr4:88157675..88159786,2	K562	blood:
2	chr4:88080087..88082421-chr4:88086230..88088491,2	K562	blood:
3	chr4:88080730..88082898-chr4:88152157..88153805,2	K562	blood:

Variant related genes	Relation type
ENSG00000248196	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10049549	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10050249	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12710836	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13105620	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13126252	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13134294	0.81[AMR][1000 genomes]
rs13134907	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13140294	0.81[AMR][1000 genomes]
rs13143182	0.80[AMR][1000 genomes]
rs13145898	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13435811	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17704256	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17755195	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2035404	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2054611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28390247	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28523549	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28621526	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28655413	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28773027	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34128785	0.81[AMR][1000 genomes]
rs34242006	0.81[AMR][1000 genomes]
rs34422965	0.81[AMR][1000 genomes]
rs34589806	0.81[AMR][1000 genomes]
rs35133616	0.81[AMR][1000 genomes]
rs35534149	0.80[AMR][1000 genomes]
rs35542725	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36123985	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71607405	0.84[AMR][1000 genomes]
rs71607407	0.80[AMR][1000 genomes]
rs71607410	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999554	0.96[AMR][1000 genomes];0.95[EUR][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	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
6	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv879526	chr4:88062611-88087832	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28668976	MAPKAPK5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:88056600-88090600	Weak transcription	Brain Angular Gyrus	brain
3	chr4:88058200-88082400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:88058200-88109000	Weak transcription	Lung	lung
5	chr4:88058600-88084200	Weak transcription	Brain Anterior Caudate	brain
6	chr4:88058800-88082400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:88058800-88088400	Weak transcription	Thymus	Thymus
8	chr4:88058800-88092200	Weak transcription	Colonic Mucosa	Colon
9	chr4:88059000-88086600	Weak transcription	A549	lung
10	chr4:88059200-88087800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:88059200-88088000	Weak transcription	Fetal Stomach	stomach
12	chr4:88059200-88100800	Weak transcription	Osteobl	bone
13	chr4:88061400-88084000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:88062600-88084400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:88063000-88090800	Weak transcription	Left Ventricle	heart
17	chr4:88063000-88090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:88063200-88088400	Weak transcription	Ovary	ovary
19	chr4:88063200-88097400	Weak transcription	Small Intestine	intestine
20	chr4:88063200-88102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:88063800-88083600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:88063800-88087800	Weak transcription	Primary T cells from cord blood	blood
23	chr4:88064200-88082800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:88064200-88090000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:88064200-88098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:88064200-88100400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:88064400-88084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:88064400-88092600	Weak transcription	HUVEC	blood vessel
29	chr4:88065600-88088200	Weak transcription	GM12878-XiMat	blood
30	chr4:88066200-88097200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:88066200-88101000	Weak transcription	HMEC	breast
32	chr4:88066600-88082800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:88066600-88082800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:88066600-88084000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:88066600-88089800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:88066800-88084200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:88066800-88084400	Weak transcription	K562	blood
38	chr4:88066800-88084600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:88066800-88093000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:88067000-88089400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:88067400-88083000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:88067600-88082600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:88067600-88084400	Weak transcription	Primary B cells from cord blood	blood
44	chr4:88067600-88087400	Weak transcription	Fetal Thymus	thymus
45	chr4:88067600-88096800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:88067800-88084400	Weak transcription	Dnd41	blood
47	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:88068200-88087000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:88068600-88084200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:88073000-88087600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links