Variant report

Variant	rs12591430
Chromosome Location	chr15:57416825-57416826
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	chr15:57410833..57413680-chr15:57416630..57418139,2	K562	blood:
2	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10467927	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10467928	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10467929	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11071308	0.82[EUR][1000 genomes]
rs12101455	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379847	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16977243	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16977270	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1841697	0.84[EUR][1000 genomes]
rs2169467	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593211	0.86[EUR][1000 genomes]
rs2593249	0.86[EUR][1000 genomes]
rs2593250	0.86[EUR][1000 genomes]
rs2593252	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703614	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2733333	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2733334	0.87[EUR][1000 genomes]
rs28372003	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28514688	0.82[AFR][1000 genomes]
rs28648502	0.82[AFR][1000 genomes]
rs28712697	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28781690	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58479554	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493900	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67077316	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163267	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7168387	0.82[AFR][1000 genomes]
rs7169508	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023736	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8034502	0.86[EUR][1000 genomes]
rs8035916	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9806170	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806199	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12591430	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs12591430	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:57382800-57419600	Weak transcription	K562	blood
3	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
6	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
14	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
17	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
18	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:57410400-57425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:57410600-57419800	Weak transcription	HepG2	liver
21	chr15:57410600-57421600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:57410600-57424800	Weak transcription	HSMMtube	muscle
23	chr15:57410600-57425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:57410600-57425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:57410600-57426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:57410600-57440800	Weak transcription	Ovary	ovary
27	chr15:57410800-57425000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:57410800-57425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:57410800-57425600	Weak transcription	HMEC	breast
30	chr15:57411000-57428200	Weak transcription	NHLF	lung
31	chr15:57411000-57430400	Weak transcription	NH-A	brain
32	chr15:57411200-57422000	Weak transcription	Hela-S3	cervix
33	chr15:57411400-57426200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:57411600-57424200	Weak transcription	Brain Germinal Matrix	brain
35	chr15:57411800-57424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:57412200-57417200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:57412400-57425000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:57412600-57424800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:57413200-57420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:57413600-57425400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:57413800-57421200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:57413800-57426600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:57413800-57428800	Weak transcription	Gastric	stomach
44	chr15:57414000-57424200	Strong transcription	Fetal Thymus	thymus
45	chr15:57414000-57425400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:57414000-57425400	Weak transcription	Left Ventricle	heart
47	chr15:57414000-57425400	Weak transcription	Small Intestine	intestine
48	chr15:57414600-57423800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:57414800-57421600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:57414800-57421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links