Variant report

Variant	rs2248886
Chromosome Location	chr15:57594933-57594934
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:57594929-57595355	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:57591325-57596303	NB4	blood:	n/a	n/a
3	POLR2A	chr15:57594222-57595937	HL-60	blood:	n/a	n/a
4	REST	chr15:57594769-57595482	HL-60	blood:	n/a	n/a
5	POLR2A	chr15:57592667-57596467	HL-60	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57588417..57590307-chr15:57592744..57595404,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-1	chr15:57592198-57595211	XLOC_011264
2	lnc-TCF12-1	chr15:57594547-57595211	XLOC_011264
3	lnc-TCF12-1	chr15:57594499-57595211	XLOC_011264
4	lnc-TCF12-1	chr15:57593541-57595211	NONHSAT044059

No data

Variant related genes	Relation type
LINC00926	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2243504	0.84[ASN][1000 genomes]
rs2414500	0.84[ASN][1000 genomes]
rs2544129	0.97[ASN][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	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
2	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
3	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2248886	LINC00926	cis	Adipose Subcutaneous	GTEx
rs2248886	LINC00926	cis	Artery Aorta	GTEx
rs2248886	LINC00926	cis	Muscle Skeletal	GTEx
rs2248886	LINC00926	cis	Nerve Tibial	GTEx
rs2248886	LINC00926	cis	Esophagus Muscularis	GTEx
rs2248886	LINC00926	cis	Skin Sun Exposed Lower leg	GTEx
rs2248886	LINC00926	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
2	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
3	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
7	chr15:57580000-57598400	Weak transcription	NHEK	skin
8	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
11	chr15:57583600-57598000	Weak transcription	Liver	Liver
12	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:57583600-57598400	Weak transcription	A549	lung
14	chr15:57583800-57595400	Weak transcription	Aorta	Aorta
15	chr15:57583800-57596800	Weak transcription	Fetal Intestine Large	intestine
16	chr15:57584000-57598200	Weak transcription	Brain Germinal Matrix	brain
17	chr15:57584400-57598000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:57584400-57598200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:57584600-57598200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:57584600-57598200	Weak transcription	Fetal Stomach	stomach
21	chr15:57585000-57598400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:57585600-57598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:57585800-57598200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:57589200-57598200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:57589400-57595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:57589400-57598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:57589400-57598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:57589600-57595200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:57589600-57598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:57589600-57598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:57590000-57597000	Weak transcription	Fetal Intestine Small	intestine
32	chr15:57590000-57598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:57590000-57598200	Weak transcription	Pancreas	Pancrea
34	chr15:57590800-57598200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:57591000-57598000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:57591600-57595400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:57591600-57598200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:57591800-57596800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:57591800-57598000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:57592000-57598000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:57592000-57598400	Weak transcription	HSMMtube	muscle
42	chr15:57592200-57597400	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:57592200-57598200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:57592200-57598400	Weak transcription	HMEC	breast
45	chr15:57592200-57598400	Weak transcription	NHLF	lung
46	chr15:57592400-57595000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:57592400-57598000	Weak transcription	Fetal Lung	lung
48	chr15:57592400-57598000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:57592400-57598200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:57592400-57598200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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