Variant report

Variant	rs2169465
Chromosome Location	chr15:57422552-57422553
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10518894	0.93[ASN][1000 genomes]
rs10518895	0.91[ASN][1000 genomes]
rs11071305	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635645	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11636100	0.94[ASN][1000 genomes]
rs11852340	0.95[ASN][1000 genomes]
rs11853331	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855648	0.91[ASN][1000 genomes]
rs12899904	0.93[ASN][1000 genomes]
rs12900038	0.93[ASN][1000 genomes]
rs12900589	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12900874	0.86[EUR][1000 genomes]
rs12903578	0.84[ASN][1000 genomes]
rs12909402	0.93[ASN][1000 genomes]
rs12910094	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12910170	0.94[ASN][1000 genomes]
rs12912007	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914182	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914410	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915473	0.84[ASN][1000 genomes]
rs13313455	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2169466	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264904	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414494	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439919	0.86[EUR][1000 genomes]
rs2585112	0.80[EUR][1000 genomes]
rs2615231	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703576	0.81[EUR][1000 genomes]
rs2703577	0.81[EUR][1000 genomes]
rs2703580	0.81[EUR][1000 genomes]
rs2733185	0.81[EUR][1000 genomes]
rs2733188	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2733307	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733332	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733341	0.81[EUR][1000 genomes]
rs28414972	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28514688	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28648502	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920269	0.82[EUR][1000 genomes]
rs2927189	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951898	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2951899	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2951903	0.83[EUR][1000 genomes]
rs2951904	0.81[EUR][1000 genomes]
rs2957591	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774910	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493901	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7168387	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173936	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8037901	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967514	0.94[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2169465	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
5	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
7	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:57406800-57425000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:57406800-57425400	Weak transcription	Pancreas	Pancrea
13	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
16	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
17	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:57410400-57425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:57410600-57424800	Weak transcription	HSMMtube	muscle
20	chr15:57410600-57425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:57410600-57425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:57410600-57426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:57410600-57440800	Weak transcription	Ovary	ovary
24	chr15:57410800-57425000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:57410800-57425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:57410800-57425600	Weak transcription	HMEC	breast
27	chr15:57411000-57428200	Weak transcription	NHLF	lung
28	chr15:57411000-57430400	Weak transcription	NH-A	brain
29	chr15:57411400-57426200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:57411600-57424200	Weak transcription	Brain Germinal Matrix	brain
31	chr15:57411800-57424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:57412400-57425000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:57412600-57424800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:57413600-57425400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:57413800-57426600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:57413800-57428800	Weak transcription	Gastric	stomach
37	chr15:57414000-57424200	Strong transcription	Fetal Thymus	thymus
38	chr15:57414000-57425400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:57414000-57425400	Weak transcription	Left Ventricle	heart
40	chr15:57414000-57425400	Weak transcription	Small Intestine	intestine
41	chr15:57414600-57423800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:57415000-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:57415000-57427800	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:57415000-57428400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:57415000-57438800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:57415200-57425000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:57415200-57425600	Weak transcription	Aorta	Aorta
48	chr15:57415400-57423000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:57415400-57423200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:57415400-57425200	Weak transcription	NHDF-Ad	bronchial

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