Variant report

Variant	rs12910109
Chromosome Location	chr15:57572148-57572149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11629653	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630910	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11631084	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11634352	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11635440	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636340	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856073	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857507	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11857722	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902099	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902581	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903221	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904189	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904933	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12908278	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909696	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911256	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911297	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912868	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12915489	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1545728	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17239508	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278685	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431023	0.87[ASN][1000 genomes]
rs2441925	0.88[ASN][1000 genomes]
rs2593235	0.84[ASN][1000 genomes]
rs3794613	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4238321	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4238322	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4303429	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4353440	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4369592	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4447362	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774251	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774252	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774918	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774919	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5014892	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61996955	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61996957	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs898901	0.81[ASN][1000 genomes]
rs935326	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960946	0.81[AMR][1000 genomes];0.88[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	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
2	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
3	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12910109	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
3	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
4	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
6	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:57544600-57574800	Weak transcription	Fetal Brain Male	brain
8	chr15:57546000-57580600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:57548200-57578000	Weak transcription	Fetal Heart	heart
10	chr15:57552200-57573200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:57552400-57578600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:57553200-57585000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:57556200-57580600	Weak transcription	Stomach Mucosa	stomach
15	chr15:57557000-57584600	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:57557600-57578000	Weak transcription	Pancreas	Pancrea
17	chr15:57557600-57588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:57558200-57573600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:57562600-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:57562600-57578000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:57562600-57584200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:57562600-57584600	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:57564000-57582400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:57564000-57583600	Strong transcription	Dnd41	blood
25	chr15:57564800-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:57564800-57584600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:57565000-57576400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:57565000-57583400	Strong transcription	Thymus	Thymus
29	chr15:57565200-57574600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:57565200-57575200	Strong transcription	Fetal Lung	lung
31	chr15:57565600-57584600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:57565800-57578000	Weak transcription	Right Ventricle	heart
33	chr15:57566000-57573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:57566000-57573600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr15:57566000-57573600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:57566000-57574400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:57566000-57577800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:57566000-57577800	Weak transcription	Brain Substantia Nigra	brain
39	chr15:57566000-57579000	Weak transcription	Brain Germinal Matrix	brain
40	chr15:57566000-57584400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
42	chr15:57566200-57573600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:57566200-57578400	Weak transcription	Spleen	Spleen
44	chr15:57566400-57573400	Weak transcription	GM12878-XiMat	blood
45	chr15:57566400-57577800	Weak transcription	Small Intestine	intestine
46	chr15:57566400-57578000	Weak transcription	Ovary	ovary
47	chr15:57567000-57574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:57567000-57579000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:57567400-57574000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr15:57567400-57575800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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