Variant report

Variant	rs28490139
Chromosome Location	chr15:57369850-57369851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6493900	0.81[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28490139	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs28490139	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57336600-57371800	Weak transcription	K562	blood
3	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
9	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:57350400-57374000	Weak transcription	Ovary	ovary
11	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
14	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:57354600-57371600	Weak transcription	NH-A	brain
17	chr15:57355000-57374000	Weak transcription	Osteobl	bone
18	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
19	chr15:57356400-57370800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:57356400-57371000	Weak transcription	Dnd41	blood
21	chr15:57356400-57371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:57356600-57372000	Weak transcription	Primary B cells from cord blood	blood
24	chr15:57356800-57371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:57357600-57371600	Weak transcription	HUVEC	blood vessel
26	chr15:57360200-57371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:57360400-57372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:57360600-57371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:57362400-57371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:57362800-57371000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:57362800-57384200	Weak transcription	HepG2	liver
32	chr15:57363000-57372600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:57363200-57371600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:57363800-57378200	Weak transcription	Gastric	stomach
35	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
36	chr15:57364800-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:57365000-57371600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:57365200-57370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:57365200-57370800	Strong transcription	Fetal Thymus	thymus
40	chr15:57365200-57374200	Weak transcription	Fetal Kidney	kidney
41	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:57365400-57370600	Weak transcription	Primary T cells from cord blood	blood
43	chr15:57365400-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:57365400-57371400	Weak transcription	GM12878-XiMat	blood
45	chr15:57365400-57371600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:57365400-57371800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:57365400-57372400	Weak transcription	Fetal Heart	heart
48	chr15:57365400-57372600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:57365400-57374000	Weak transcription	NHEK	skin
50	chr15:57365600-57371600	Weak transcription	Muscle Satellite Cultured Cells	--

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