Variant report

Variant	rs12710836
Chromosome Location	chr4:88136888-88136889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88135352..88139802-chr4:88139863..88143075,5	MCF-7	breast:
2	chr4:88122650..88125039-chr4:88136374..88138823,2	K562	blood:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10049549	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13105620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13126252	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134294	0.84[AMR][1000 genomes]
rs13134907	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13140294	0.84[AMR][1000 genomes]
rs13143182	1.00[LWK][hapmap];0.84[TSI][hapmap]
rs13145898	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435811	1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17704256	1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17755195	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035404	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2054611	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28390247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28523549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668976	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28773027	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34128785	0.84[AMR][1000 genomes]
rs34242006	0.84[AMR][1000 genomes]
rs34422965	0.84[AMR][1000 genomes]
rs34589806	0.84[AMR][1000 genomes]
rs35133616	0.84[AMR][1000 genomes]
rs35542725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36123985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71607405	0.80[AMR][1000 genomes]
rs71607410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12710836	KLHL8	cis	multi-tissue	Pritchard
rs12710836	MAPKAPK5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
2	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:88116400-88138000	Weak transcription	HepG2	liver
4	chr4:88122400-88140000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:88125400-88140200	Weak transcription	Fetal Intestine Large	intestine
6	chr4:88126800-88140000	Weak transcription	Fetal Stomach	stomach
7	chr4:88127200-88140200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:88128400-88140000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:88128600-88140000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:88128600-88140200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:88129400-88139800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:88129800-88140000	Weak transcription	Fetal Intestine Small	intestine
13	chr4:88130600-88140000	Weak transcription	Fetal Brain Female	brain
14	chr4:88130800-88139800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:88131200-88140200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:88131400-88137200	Weak transcription	GM12878-XiMat	blood
17	chr4:88132000-88139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:88132000-88140200	Weak transcription	Primary B cells from cord blood	blood
19	chr4:88132200-88139200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:88133200-88140000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:88134800-88140800	Weak transcription	Spleen	Spleen
22	chr4:88135000-88139800	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:88135000-88140000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:88135000-88140000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:88135000-88140200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:88135000-88140200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:88135000-88140200	Weak transcription	Pancreas	Pancrea
28	chr4:88135000-88140200	Weak transcription	Right Ventricle	heart
29	chr4:88135000-88140200	Weak transcription	Stomach Mucosa	stomach
30	chr4:88135200-88139800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:88135200-88139800	Weak transcription	Adipose Nuclei	Adipose
32	chr4:88135200-88139800	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:88135200-88140000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:88135200-88140000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:88135200-88140000	Weak transcription	Left Ventricle	heart
36	chr4:88135200-88140000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:88135200-88140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:88135200-88140000	Weak transcription	Hela-S3	cervix
39	chr4:88135200-88140200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:88135200-88140200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:88135200-88140200	Weak transcription	Brain Germinal Matrix	brain
42	chr4:88135200-88140200	Weak transcription	Fetal Heart	heart
43	chr4:88135200-88140200	Weak transcription	Fetal Lung	lung
44	chr4:88135200-88140200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:88135200-88140200	Weak transcription	A549	lung
46	chr4:88135200-88140200	Weak transcription	NHEK	skin
47	chr4:88135200-88140400	Weak transcription	Psoas Muscle	Psoas
48	chr4:88135200-88140400	Weak transcription	Right Atrium	heart
49	chr4:88135200-88140400	Weak transcription	Small Intestine	intestine
50	chr4:88135400-88138400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links