Variant report

Variant	rs2406568
Chromosome Location	chr12:42552297-42552298
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42536641..42539823-chr12:42545599..42552985,7	MCF-7	breast:
2	chr12:42538421..42542265-chr12:42549235..42553019,4	K562	blood:

Variant related genes	Relation type
ENSG00000151233	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459290	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492388	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1059360	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880256	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880258	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880260	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880268	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880269	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880272	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880273	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181364	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181378	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181380	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181398	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181399	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12049942	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12308219	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366848	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12370778	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371615	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371762	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406567	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582390	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582391	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138877	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315968	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957471	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965392	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7974476	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974654	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9668610	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2406568	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs2406568	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
6	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:42539600-42552400	Weak transcription	HUVEC	blood vessel
8	chr12:42539600-42553600	Weak transcription	Adipose Nuclei	Adipose
9	chr12:42539600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:42539600-42553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
12	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
13	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
15	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:42539800-42553000	Weak transcription	Hela-S3	cervix
17	chr12:42539800-42554200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
20	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
21	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
22	chr12:42540000-42553800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine
24	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:42541200-42553600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:42545200-42553800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:42545400-42554200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:42545600-42553200	Weak transcription	NH-A	brain
29	chr12:42546000-42564400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:42546400-42553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:42546600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:42547200-42553000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:42547200-42563800	Weak transcription	Fetal Stomach	stomach
34	chr12:42547600-42554000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:42548200-42553800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:42548400-42553000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:42548400-42553800	Weak transcription	Osteobl	bone
39	chr12:42548800-42552400	Weak transcription	Dnd41	blood
40	chr12:42549200-42553600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:42549400-42575000	Weak transcription	Brain Angular Gyrus	brain
42	chr12:42549800-42553400	Weak transcription	HepG2	liver
43	chr12:42550200-42553800	Weak transcription	Liver	Liver
44	chr12:42550200-42555400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:42550400-42553400	Weak transcription	NHDF-Ad	bronchial
46	chr12:42550400-42556200	Weak transcription	Fetal Heart	heart
47	chr12:42550600-42554200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:42550600-42554200	Weak transcription	Fetal Intestine Large	intestine
49	chr12:42550600-42555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:42550600-42557400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links