Variant report

Variant	rs28445470
Chromosome Location	chr15:57551577-57551578
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57548795..57550797-chr15:57550821..57552901,2	K562	blood:
2	chr15:57548444..57552670-chr15:57553195..57556981,4	K562	blood:
3	chr15:57543333..57548085-chr15:57548138..57552930,5	K562	blood:
4	chr15:57546353..57548188-chr15:57549321..57552390,3	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11853810	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856210	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16977278	0.83[ASN][1000 genomes]
rs16977306	0.81[EUR][1000 genomes]
rs16977374	0.94[ASN][1000 genomes]
rs2615226	0.96[ASN][1000 genomes]
rs2615227	0.98[ASN][1000 genomes]
rs2733323	0.81[ASN][1000 genomes]
rs28536671	0.81[EUR][1000 genomes]
rs28653088	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803453	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774915	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774916	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55742030	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493907	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163126	0.81[EUR][1000 genomes]
rs7164298	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164914	0.88[ASN][1000 genomes]
rs7173477	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173748	0.83[ASN][1000 genomes]
rs7180558	0.99[ASN][1000 genomes]
rs7181399	0.82[EUR][1000 genomes]
rs8024901	0.95[ASN][1000 genomes]
rs8026702	0.85[ASN][1000 genomes]
rs8034744	0.82[EUR][1000 genomes]
rs8034843	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037956	0.95[ASN][1000 genomes]
rs8039176	0.95[ASN][1000 genomes]
rs9672676	0.81[EUR][1000 genomes]
rs997683	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28445470	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	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
5	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
6	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
7	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
9	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:57528400-57554800	Weak transcription	NHEK	skin
11	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:57537800-57551600	Weak transcription	Brain Germinal Matrix	brain
14	chr15:57537800-57551800	Weak transcription	Small Intestine	intestine
15	chr15:57537800-57555200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
17	chr15:57538400-57551800	Weak transcription	Stomach Mucosa	stomach
18	chr15:57538400-57564800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:57538600-57551800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:57538800-57554200	Weak transcription	Fetal Brain Female	brain
21	chr15:57539400-57554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:57539600-57556800	Weak transcription	Gastric	stomach
24	chr15:57539600-57565200	Weak transcription	Aorta	Aorta
25	chr15:57539600-57565200	Weak transcription	Esophagus	oesophagus
26	chr15:57540000-57554400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:57540200-57551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:57540200-57555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:57540600-57551800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:57540600-57556800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:57540600-57557000	Weak transcription	Lung	lung
32	chr15:57540600-57565400	Weak transcription	Ovary	ovary
33	chr15:57543000-57556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:57543200-57565200	Weak transcription	Right Ventricle	heart
35	chr15:57544400-57551600	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:57544400-57551600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:57544400-57551800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:57544600-57574800	Weak transcription	Fetal Brain Male	brain
39	chr15:57545800-57551600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:57545800-57551600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:57545800-57554400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:57545800-57554400	Weak transcription	HMEC	breast
43	chr15:57545800-57554600	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:57545800-57565200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:57546000-57551600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:57546000-57553800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:57546000-57554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:57546000-57554400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:57546000-57554400	Weak transcription	A549	lung
50	chr15:57546000-57580600	Weak transcription	Placenta Amnion	Placenta Amnion

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