Variant report

Variant	rs898901
Chromosome Location	chr15:57538765-57538766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57519601..57521233-chr15:57537567..57539134,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1037956	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037958	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10518899	0.87[EUR][1000 genomes]
rs11071309	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11629653	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630910	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631084	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632069	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11633061	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11634352	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635440	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11636201	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11636340	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636348	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11636919	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11637955	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856055	0.84[EUR][1000 genomes]
rs11856073	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857507	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857722	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11858783	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12050751	0.86[EUR][1000 genomes]
rs12050758	0.86[EUR][1000 genomes]
rs12898356	0.85[EUR][1000 genomes]
rs12899036	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12899588	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901671	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12902099	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12902170	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902581	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903115	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12903151	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903221	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904189	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904321	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904501	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904561	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904602	0.84[EUR][1000 genomes]
rs12904933	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906042	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12906335	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906566	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908278	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908760	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909016	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909696	0.80[ASN][1000 genomes]
rs12910109	0.81[ASN][1000 genomes]
rs12910556	0.84[EUR][1000 genomes]
rs12910832	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12911256	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911297	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911518	0.88[EUR][1000 genomes]
rs12912210	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912353	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912392	0.83[EUR][1000 genomes]
rs12912868	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914425	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914481	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915489	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916478	0.88[EUR][1000 genomes]
rs12917093	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1462156	0.88[EUR][1000 genomes]
rs1545728	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17239431	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17239508	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814585	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1867641	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2278685	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290938	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2414491	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2414492	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2414497	0.84[EUR][1000 genomes]
rs2431023	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2441925	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2593235	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2593237	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2593238	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3794613	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238321	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238322	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4303429	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4353440	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369592	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4447362	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774250	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774251	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774252	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774913	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774918	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774919	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5014892	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61996955	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61996957	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62022237	0.84[ASN][1000 genomes]
rs7161965	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs745652	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs935326	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs960946	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs978274	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv974581	chr15:57538491-57540100	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs898901	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	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
7	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
8	chr15:57524400-57540600	Strong transcription	Primary T cells from cord blood	blood
9	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
10	chr15:57526000-57539000	Weak transcription	Gastric	stomach
11	chr15:57526000-57539200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:57526000-57539200	Weak transcription	Lung	lung
13	chr15:57526000-57542600	Weak transcription	Right Ventricle	heart
14	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:57526400-57539200	Weak transcription	Aorta	Aorta
16	chr15:57526600-57539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
20	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:57528400-57554800	Weak transcription	NHEK	skin
25	chr15:57528600-57539000	Weak transcription	A549	lung
26	chr15:57529000-57545400	Weak transcription	HMEC	breast
27	chr15:57529400-57543400	Weak transcription	HUVEC	blood vessel
28	chr15:57529600-57540000	Weak transcription	Fetal Heart	heart
29	chr15:57530200-57543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:57531000-57542400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:57531400-57541200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:57531600-57540200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:57535000-57539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:57535000-57540000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:57535000-57541200	Strong transcription	NH-A	brain
38	chr15:57535200-57540000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:57535200-57542600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:57535400-57540000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:57535400-57540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:57535600-57539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:57535600-57539600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:57535600-57539800	Strong transcription	Adipose Nuclei	Adipose
45	chr15:57535600-57540200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:57535600-57540200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:57535600-57540200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:57535600-57540400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:57535600-57540400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr15:57535600-57540600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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