Variant report

Variant	rs2249219
Chromosome Location	chr15:57591871-57591872
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:57591676-57591988	A549	lung:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
2	RUNX3	chr15:57591661-57592548	GM12878	blood:	n/a	n/a
3	CEBPB	chr15:57591725-57591939	MCF-7	breast:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
4	WRNIP1	chr15:57591555-57592415	GM12878	blood:	n/a	n/a
5	RELA	chr15:57591857-57592952	GM15510	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
6	POLR2A	chr15:57591063-57592554	HL-60	blood:	n/a	n/a
7	POLR2A	chr15:57591325-57596303	NB4	blood:	n/a	n/a
8	CEBPB	chr15:57591670-57592038	A549	lung:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
9	MAX	chr15:57591131-57593104	NB4	blood:	n/a	n/a
10	RELA	chr15:57591673-57593287	GM19193	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
11	CEBPB	chr15:57591676-57592033	HepG2	liver:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
12	MTA3	chr15:57591568-57592581	GM12878	blood:	n/a	n/a
13	CEBPB	chr15:57591716-57591988	Hela-S3	cervix:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
14	FOXM1	chr15:57591850-57592399	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:57591446-57594099	GM12891	blood:	n/a	n/a
16	NFIC	chr15:57591827-57592573	GM12878	blood:	n/a	n/a
17	CEBPB	chr15:57591708-57592025	H1-hESC	embryonic stem cell:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
18	CEBPB	chr15:57591674-57592050	IMR90	lung:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
19	CEBPB	chr15:57591671-57592095	K562	blood:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
20	POU2F2	chr15:57591865-57592711	GM12878	blood:	n/a	n/a
21	ATF2	chr15:57591803-57592469	GM12878	blood:	n/a	n/a
22	RELA	chr15:57591779-57592998	GM18505	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
23	POLR2A	chr15:57591152-57593018	GM19193	blood:	n/a	n/a
24	RELA	chr15:57591814-57592659	GM12878	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
25	POLR2A	chr15:57591426-57592562	HL-60	blood:	n/a	n/a
26	RELA	chr15:57591502-57592979	GM19099	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
27	RUNX3	chr15:57591848-57592547	GM12878	blood:	n/a	n/a
28	SPI1	chr15:57591640-57592687	GM12878	blood:	n/a	chr15:57591726-57591739
29	SP1	chr15:57591870-57592542	GM12878	blood:	n/a	n/a
30	CEBPB	chr15:57591694-57591988	K562	blood:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
31	BCLAF1	chr15:57591812-57592569	GM12878	blood:	n/a	chr15:57592091-57592104 chr15:57592122-57592131
32	RELA	chr15:57591853-57592601	GM12892	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
33	RELA	chr15:57591638-57593023	GM18951	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
34	POLR2A	chr15:57591163-57594122	GM12878	blood:	n/a	n/a
35	PAX5	chr15:57591836-57592423	GM12878	blood:	n/a	n/a
36	ELF1	chr15:57591852-57592554	GM12878	blood:	n/a	n/a
37	RELA	chr15:57591186-57592673	GM12891	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
38	POLR2A	chr15:57591597-57593159	Raji	blood:	n/a	n/a
39	SPI1	chr15:57591846-57592506	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57582135..57584182-chr15:57589221..57591985,2	K562	blood:
2	chr15:57582041..57585604-chr15:57586782..57591985,5	K562	blood:

Variant related genes	Relation type
LINC00926	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11629673	1.00[JPT][hapmap]
rs17819964	1.00[JPT][hapmap]
rs2243451	1.00[JPT][hapmap]
rs2244509	1.00[JPT][hapmap]
rs2244772	1.00[JPT][hapmap]
rs2247485	1.00[JPT][hapmap]
rs2248534	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2440943	1.00[JPT][hapmap]
rs6493912	0.83[CEU][hapmap];1.00[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2249219	LINC00926	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 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	chr15:57578800-57592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:57579200-57592800	Weak transcription	Small Intestine	intestine
5	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
9	chr15:57580000-57598400	Weak transcription	NHEK	skin
10	chr15:57580600-57594800	Weak transcription	HepG2	liver
11	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
14	chr15:57583600-57598000	Weak transcription	Liver	Liver
15	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:57583600-57598400	Weak transcription	A549	lung
17	chr15:57583800-57595400	Weak transcription	Aorta	Aorta
18	chr15:57583800-57596800	Weak transcription	Fetal Intestine Large	intestine
19	chr15:57584000-57598200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:57584400-57598000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:57584400-57598200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:57584600-57594600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:57584600-57598200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:57584600-57598200	Weak transcription	Fetal Stomach	stomach
25	chr15:57585000-57598400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:57585600-57598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57585800-57598200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:57588400-57593000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:57589200-57598200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:57589400-57592000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr15:57589400-57592400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:57589400-57594800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:57589400-57595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:57589400-57598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:57589400-57598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:57589600-57595200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:57589600-57598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:57589600-57598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:57589800-57592800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:57590000-57592000	Weak transcription	Stomach Mucosa	stomach
41	chr15:57590000-57592800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:57590000-57597000	Weak transcription	Fetal Intestine Small	intestine
43	chr15:57590000-57598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:57590000-57598200	Weak transcription	Pancreas	Pancrea
45	chr15:57590400-57592400	Enhancers	Fetal Lung	lung
46	chr15:57590400-57593600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr15:57590800-57592000	Enhancers	HSMMtube	muscle
48	chr15:57590800-57592400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:57590800-57598200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:57591000-57592200	Enhancers	Fetal Muscle Leg	muscle

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