Variant report

Variant	rs12915473
Chromosome Location	chr15:57455320-57455321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1037956	0.80[ASN][1000 genomes]
rs1037958	0.80[ASN][1000 genomes]
rs10518895	0.83[ASN][1000 genomes]
rs10518899	0.82[EUR][1000 genomes]
rs11071305	0.85[EUR][1000 genomes]
rs11071309	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11630195	0.83[AMR][1000 genomes]
rs11631541	0.82[AMR][1000 genomes]
rs11632069	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633061	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11636201	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636348	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636919	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637955	0.80[ASN][1000 genomes]
rs11853331	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855648	0.83[ASN][1000 genomes]
rs11856055	0.82[EUR][1000 genomes]
rs11858783	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12050751	0.82[EUR][1000 genomes]
rs12050758	0.82[EUR][1000 genomes]
rs12898327	0.85[AMR][1000 genomes]
rs12898356	0.84[EUR][1000 genomes]
rs12899036	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12899187	0.81[AMR][1000 genomes]
rs12899588	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899904	0.83[ASN][1000 genomes]
rs12899915	0.83[AMR][1000 genomes]
rs12900038	0.85[ASN][1000 genomes]
rs12901671	0.80[ASN][1000 genomes]
rs12902170	0.80[ASN][1000 genomes]
rs12903115	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12903578	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904321	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904501	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904561	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12904602	0.85[EUR][1000 genomes]
rs12905900	0.84[AMR][1000 genomes]
rs12906042	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906335	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12906566	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12906873	0.83[AMR][1000 genomes]
rs12906936	0.83[AMR][1000 genomes]
rs12908760	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12909811	0.81[AMR][1000 genomes]
rs12910094	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910556	0.85[EUR][1000 genomes]
rs12910832	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911518	0.81[EUR][1000 genomes]
rs12912007	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12912210	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912353	0.80[ASN][1000 genomes]
rs12912392	0.84[EUR][1000 genomes]
rs12914182	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12914410	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914425	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914481	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12916478	0.81[EUR][1000 genomes]
rs12916958	0.81[AMR][1000 genomes]
rs12917247	0.83[AMR][1000 genomes]
rs1430823	0.84[AMR][1000 genomes]
rs1462156	0.81[EUR][1000 genomes]
rs17239040	0.83[AMR][1000 genomes]
rs1814585	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1867641	0.80[ASN][1000 genomes]
rs2169465	0.84[ASN][1000 genomes]
rs2290938	0.80[ASN][1000 genomes]
rs2414491	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414494	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2414497	0.85[EUR][1000 genomes]
rs2593237	0.82[EUR][1000 genomes]
rs2593238	0.82[EUR][1000 genomes]
rs2733176	0.81[AMR][1000 genomes]
rs2733341	0.85[ASN][1000 genomes]
rs35646942	0.81[AMR][1000 genomes]
rs4774250	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774910	0.89[EUR][1000 genomes]
rs4774913	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62022237	0.80[ASN][1000 genomes]
rs62022986	0.81[AMR][1000 genomes]
rs62022988	0.84[AMR][1000 genomes]
rs6493901	0.89[EUR][1000 genomes]
rs7161965	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs745652	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8037901	0.81[ASN][1000 genomes]
rs978274	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv977056	chr15:57451639-57455991	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12915473	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:57439400-57456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:57444200-57456600	Strong transcription	Fetal Thymus	thymus
5	chr15:57444400-57459000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:57444400-57459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:57444400-57485600	Weak transcription	Placenta	Placenta
8	chr15:57444400-57507400	Weak transcription	K562	blood
9	chr15:57444600-57455600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:57444600-57458000	Weak transcription	Dnd41	blood
11	chr15:57444600-57458400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:57444600-57459000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:57444600-57459600	Weak transcription	Liver	Liver
14	chr15:57444600-57490200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:57444800-57458600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:57444800-57458800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:57444800-57458800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:57444800-57484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:57444800-57484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:57445000-57455600	Weak transcription	Primary T cells from cord blood	blood
21	chr15:57445000-57461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:57445200-57466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:57445400-57458800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:57445400-57478400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:57445600-57455800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:57445600-57458800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:57445600-57459000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:57445600-57461400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:57446000-57455600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:57446000-57455600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr15:57446000-57468400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:57446200-57458800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:57446600-57455600	Weak transcription	Primary B cells from cord blood	blood
34	chr15:57446600-57459600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:57447000-57484600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:57447200-57458200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr15:57447800-57466000	Weak transcription	Pancreas	Pancrea
38	chr15:57448000-57465600	Weak transcription	Right Ventricle	heart
39	chr15:57448000-57483800	Weak transcription	Lung	lung
40	chr15:57448800-57460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:57448800-57463400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:57449000-57458600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:57450800-57459400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:57450800-57469000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:57450800-57491000	Weak transcription	Left Ventricle	heart
46	chr15:57451000-57458000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:57451000-57464400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:57451000-57477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:57451000-57487800	Weak transcription	Psoas Muscle	Psoas
50	chr15:57451000-57490800	Weak transcription	NHEK	skin

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