Variant report

Variant	rs2167594
Chromosome Location	chr15:45018489-45018490
allele	A/C
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	MTA3	chr15:45018115-45020373	GM12878	blood:	n/a	n/a
2	BCLAF1	chr15:45018369-45019939	GM12878	blood:	n/a	chr15:45019779-45019788
3	MYC	chr15:45018467-45018582	MCF10A-Er-Src	breast:	n/a	chr15:45018482-45018491
4	ZNF384	chr15:45018452-45020444	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:45018208-45022301	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:45017478-45022298	GM12892	blood:	n/a	n/a
7	CEBPB	chr15:45018458-45019370	Hela-S3	cervix:	n/a	n/a
8	MTA3	chr15:45018319-45020007	GM12878	blood:	n/a	n/a
9	FOS	chr15:45018483-45018625	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr15:45018456-45019126	K562	blood:	n/a	n/a
11	FOS	chr15:45018427-45019939	MCF10A-Er-Src	breast:	n/a	chr15:45019778-45019788 chr15:45019016-45019027 chr15:45019779-45019787 chr15:45019777-45019789 chr15:45019780-45019791 chr15:45019019-45019026 chr15:45019016-45019027 chr15:45019017-45019026
12	TBL1XR1	chr15:45018458-45018537	K562	blood:	n/a	n/a
13	POLR2A	chr15:45016436-45022852	GM12892	blood:	n/a	n/a
14	RELA	chr15:45018326-45020334	GM18505	blood:	n/a	chr15:45019844-45019853 chr15:45019844-45019853
15	POLR2A	chr15:45016397-45023417	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:45018274-45022504	GM18951	blood:	n/a	n/a
17	POLR2A	chr15:45018310-45022158	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:45018199-45023414	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:45017530-45022287	GM12891	blood:	n/a	n/a
20	POLR2A	chr15:45018167-45019208	GM12878	blood:	n/a	n/a
21	MYC	chr15:45018429-45019757	K562	blood:	n/a	chr15:45018482-45018491
22	BCLAF1	chr15:45018334-45020198	GM12878	blood:	n/a	chr15:45019779-45019788 chr15:45020075-45020083
23	POLR2A	chr15:45016457-45022594	GM12878	blood:	n/a	n/a
24	RELA	chr15:45018411-45020050	GM15510	blood:	n/a	chr15:45019844-45019853 chr15:45019844-45019853
25	MXI1	chr15:45018485-45020261	GM12878	blood:	n/a	n/a
26	KAT2A	chr15:45018484-45019529	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:45018391-45019836	U87	brain:	n/a	n/a
28	POLR2A	chr15:45018225-45019153	GM12878	blood:	n/a	n/a
29	ESRRA	chr15:45018311-45023010	GM12878	blood:	n/a	chr15:45021237-45021249 chr15:45021233-45021249 chr15:45021238-45021254 chr15:45021237-45021247
30	RELA	chr15:45018399-45019361	GM18951	blood:	n/a	n/a
31	POLR2A	chr15:45018237-45022545	GM12892	blood:	n/a	n/a
32	ATF2	chr15:45018387-45019976	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:45016464-45022895	GM18505	blood:	n/a	n/a
34	POU2F2	chr15:45018220-45020369	GM12878	blood:	n/a	n/a
35	RELA	chr15:45018435-45022209	GM12878	blood:	n/a	chr15:45019844-45019853 chr15:45019844-45019853
36	POLR2A	chr15:45017483-45022411	GM12892	blood:	n/a	n/a
37	POLR2A	chr15:45016449-45022997	GM12891	blood:	n/a	n/a
38	FOXM1	chr15:45018390-45020304	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:45018137-45020393	GM12891	blood:	n/a	n/a
40	RELA	chr15:45018421-45020324	GM10847	blood:	n/a	chr15:45019844-45019853 chr15:45019844-45019853
41	POLR2A	chr15:45018325-45019736	Raji	blood:	n/a	n/a
42	POLR2A	chr15:45017592-45022425	GM19193	blood:	n/a	n/a
43	POLR2A	chr15:45018294-45022406	GM18526	blood:	n/a	n/a
44	STAT3	chr15:45018416-45021926	GM12878	blood:	n/a	chr15:45021002-45021014 chr15:45021304-45021316 chr15:45021015-45021026 chr15:45021042-45021053
45	FOS	chr15:45018442-45020015	MCF10A-Er-Src	breast:	n/a	chr15:45019778-45019788 chr15:45019016-45019027 chr15:45019779-45019787 chr15:45019777-45019789 chr15:45019780-45019791 chr15:45019019-45019026 chr15:45019016-45019027 chr15:45019017-45019026
46	POLR2A	chr15:45018118-45020433	GM12891	blood:	n/a	n/a
47	BHLHE40	chr15:45018446-45022030	GM12878	blood:	n/a	n/a
48	NFIC	chr15:45018367-45022471	GM12878	blood:	n/a	chr15:45019702-45019718
49	FOXM1	chr15:45018382-45020013	GM12878	blood:	n/a	n/a
50	RELA	chr15:45018368-45020251	GM12891	blood:	n/a	chr15:45019844-45019853 chr15:45019844-45019853

No.	Distal block	Cell Line	Cell type
1	chr15:44953583..44958025-chr15:45017998..45023674,11	MCF-7	breast:
2	chr15:45003079..45005012-chr15:45015823..45018860,3	MCF-7	breast:
3	chr15:44875120..44878019-chr15:45017831..45020827,2	K562	blood:
4	chr15:44872601..44874196-chr15:45017482..45020327,2	K562	blood:
5	chr15:45007779..45009819-chr15:45018036..45020681,2	MCF-7	breast:
6	chr15:44829305..44830932-chr15:45017606..45019310,2	K562	blood:
7	chr15:45017018..45019763-chr15:45071670..45073544,3	K562	blood:
8	chr15:44952092..44957540-chr15:45017481..45022918,18	K562	blood:
9	chr10:103577767..103578618-chr15:45018317..45019222,2	Hela-S3	cervix:
10	chr15:44953895..44957741-chr15:45015371..45022655,19	K562	blood:
11	chr15:44988903..44990685-chr15:45017956..45020039,2	K562	blood:
12	chr15:45018290..45020903-chr15:45076318..45078549,2	K562	blood:
13	chr15:45018082..45020935-chr15:45038655..45041399,2	K562	blood:
14	chr15:44955531..44956428-chr15:45018462..45019007,2	MCF-7	breast:

Variant related genes	Relation type
TRIM69	TF binding region
ENSG00000229474	Chromatin interaction
ENSG00000206957	Chromatin interaction
ENSG00000198408	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000104131	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1288094	1.00[AMR][1000 genomes]
rs1669834	0.83[LWK][hapmap];1.00[MKK][hapmap]
rs1669854	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1720723	0.83[LWK][hapmap]
rs1901536	0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1901539	1.00[AMR][1000 genomes]
rs2167595	0.84[YRI][hapmap]
rs2254602	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2444005	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2444007	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2444011	1.00[AMR][1000 genomes]
rs2462044	1.00[AMR][1000 genomes]
rs2468072	1.00[AMR][1000 genomes]
rs2470916	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2960207	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3100129	1.00[AMR][1000 genomes]
rs3100130	1.00[AMR][1000 genomes]
rs3100144	1.00[AMR][1000 genomes]
rs3100145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110179	0.89[AFR][1000 genomes]
rs3110180	1.00[AMR][1000 genomes]
rs3110673	1.00[AMR][1000 genomes]
rs3110674	1.00[AMR][1000 genomes]
rs34359070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34387827	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34708122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4625702	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493125	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2167594	METT5D1	trans	lymphoblastoid	seeQTL
rs2167594	IQCG	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:45005000-45018600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:45009400-45018600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:45009400-45020000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:45009400-45020600	Weak transcription	Brain Angular Gyrus	brain
6	chr15:45009400-45020600	Weak transcription	Pancreas	Pancrea
7	chr15:45009400-45020600	Weak transcription	Right Ventricle	heart
8	chr15:45009400-45020800	Weak transcription	Aorta	Aorta
9	chr15:45009600-45020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:45009600-45020800	Weak transcription	Fetal Brain Male	brain
11	chr15:45010200-45020600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:45010200-45020600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:45010200-45020600	Weak transcription	Fetal Kidney	kidney
14	chr15:45010600-45020200	Weak transcription	Psoas Muscle	Psoas
15	chr15:45010600-45020600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:45010600-45020600	Weak transcription	Brain Substantia Nigra	brain
17	chr15:45010800-45018600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:45010800-45020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:45010800-45020600	Weak transcription	Ovary	ovary
20	chr15:45011000-45019000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:45011000-45020600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:45011000-45020600	Weak transcription	Fetal Stomach	stomach
23	chr15:45011200-45018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:45011200-45018600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:45011200-45018600	Weak transcription	HSMM	muscle
26	chr15:45011200-45018800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:45011200-45019800	Weak transcription	Brain Anterior Caudate	brain
28	chr15:45011200-45020000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:45011200-45020000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:45011400-45018600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:45011400-45020600	Weak transcription	Fetal Lung	lung
32	chr15:45011800-45020800	Weak transcription	Gastric	stomach
33	chr15:45012000-45019000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:45013200-45019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:45013200-45019800	Weak transcription	Spleen	Spleen
36	chr15:45015200-45018600	Enhancers	K562	blood
37	chr15:45015400-45021000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr15:45016000-45020600	Enhancers	Fetal Thymus	thymus
39	chr15:45016800-45021000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr15:45017000-45020400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr15:45017600-45018600	Enhancers	Hela-S3	cervix
42	chr15:45017600-45018800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:45017600-45019000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr15:45017600-45019200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:45017600-45020400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr15:45017600-45020400	Enhancers	Small Intestine	intestine
47	chr15:45017600-45020600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr15:45017800-45018600	Enhancers	Stomach Smooth Muscle	stomach
49	chr15:45017800-45019400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr15:45018000-45019000	Active TSS	GM12878-XiMat	blood

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