Variant report

Variant	rs2290330
Chromosome Location	chr15:45021227-45021228
allele	G/T
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	POLR2A	chr15:45021172-45021589	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:45020831-45021540	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr15:45020776-45021897	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:45020833-45021846	HL-60	blood:	n/a	n/a
5	TCF12	chr15:45021037-45021644	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr15:45020759-45021446	K562	blood:	n/a	n/a
7	TEAD4	chr15:45020636-45021953	K562	blood:	n/a	n/a
8	EP300	chr15:45020849-45021373	GM12878	blood:	n/a	chr15:45021261-45021270
9	RUNX3	chr15:45020575-45022208	GM12878	blood:	n/a	n/a
10	NFYA	chr15:45020896-45021547	Hela-S3	cervix:	n/a	n/a
11	GATA3	chr15:45020654-45021384	A549	lung:	n/a	n/a
12	POLR2A	chr15:45020891-45021934	PBDE	blood:	n/a	n/a
13	NFYA	chr15:45020905-45021391	K562	blood:	n/a	n/a
14	TCF7L2	chr15:45020828-45021318	MCF-7	breast:	n/a	n/a
15	REST	chr15:45020538-45022214	H1-neurons	neurons:	n/a	chr15:45021085-45021092 chr15:45021260-45021273
16	EP300	chr15:45020714-45021914	SK-N-SH	brain:	n/a	chr15:45021261-45021270 chr15:45021828-45021842
17	STAT3	chr15:45020809-45021881	MCF10A-Er-Src	breast:	n/a	chr15:45021002-45021014 chr15:45021304-45021316 chr15:45021015-45021026 chr15:45021042-45021053
18	POLR2A	chr15:45020467-45022290	GM12891	blood:	n/a	n/a
19	MXI1	chr15:45020888-45021249	K562	blood:	n/a	n/a
20	MXI1	chr15:45020692-45021856	HepG2	liver:	n/a	n/a
21	GTF2F1	chr15:45020961-45021399	K562	blood:	n/a	n/a
22	MAX	chr15:45020690-45021853	SK-N-SH	brain:	n/a	n/a
23	MAZ	chr15:45020694-45021840	K562	blood:	n/a	n/a
24	FOS	chr15:45020680-45021330	K562	blood:	n/a	chr15:45020814-45020825
25	MYC	chr15:45020644-45021777	K562	blood:	n/a	n/a
26	SIN3AK20	chr15:45020733-45021624	PANC-1	pancreas:	n/a	n/a
27	MYC	chr15:45020791-45021914	NB4	blood:	n/a	n/a
28	POLR2A	chr15:45020729-45021625	K562	blood:	n/a	n/a
29	ATF1	chr15:45020692-45021385	K562	blood:	n/a	n/a
30	TCF3	chr15:45021163-45021484	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:45018208-45022301	GM12892	blood:	n/a	n/a
32	BRCA1	chr15:45020928-45021409	HepG2	liver:	n/a	n/a
33	CEBPB	chr15:45020788-45021362	HepG2	liver:	n/a	n/a
34	MAFK	chr15:45020810-45021307	HepG2	liver:	n/a	chr15:45020959-45020976
35	POLR2A	chr15:45017478-45022298	GM12892	blood:	n/a	n/a
36	EP300	chr15:45020501-45022226	SK-N-SH	brain:	n/a	chr15:45021261-45021270 chr15:45021828-45021842
37	HCFC1	chr15:45020580-45021741	K562	blood:	n/a	n/a
38	POLR2A	chr15:45020673-45021542	K562	blood:	n/a	n/a
39	POLR2A	chr15:45020844-45021628	HepG2	liver:	n/a	n/a
40	EP300	chr15:45020583-45021752	GM12878	blood:	n/a	chr15:45021261-45021270
41	CUX1	chr15:45020823-45021351	K562	blood:	n/a	n/a
42	CHD1	chr15:45020141-45022460	IMR90	lung:	n/a	n/a
43	YY1	chr15:45021153-45021547	ECC-1	luminal epithelium:	n/a	chr15:45021261-45021270 chr15:45021258-45021267 chr15:45021259-45021273
44	PBX3	chr15:45020723-45021456	SK-N-SH	brain:	n/a	n/a
45	EP300	chr15:45020677-45021836	K562	blood:	n/a	chr15:45021261-45021270
46	MYC	chr15:45020648-45021329	MCF10A-Er-Src	breast:	n/a	n/a
47	RFX5	chr15:45020254-45021856	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr15:45020677-45021784	HepG2	liver:	n/a	n/a
49	NFYA	chr15:45020929-45021373	GM12878	blood:	n/a	n/a
50	TBL1XR1	chr15:45020662-45021915	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44953583..44958025-chr15:45017998..45023674,11	MCF-7	breast:
2	chr15:44911239..44913616-chr15:45019732..45022719,2	MCF-7	breast:
3	chr15:44952527..44956177-chr15:45018956..45022716,7	MCF-7	breast:
4	chr15:44952092..44957540-chr15:45017481..45022918,18	K562	blood:
5	chr15:44953895..44957741-chr15:45015371..45022655,19	K562	blood:
6	chr10:76970496..76971183-chr15:45020835..45021528,2	Hela-S3	cervix:
7	chr15:44958326..44960851-chr15:45019076..45021871,2	MCF-7	breast:
8	chr15:45000863..45005844-chr15:45018710..45023352,9	MCF-7	breast:
9	chr15:45004559..45007244-chr15:45019568..45021417,3	MCF-7	breast:
10	chr15:45007310..45009648-chr15:45019472..45022079,3	MCF-7	breast:
11	chr15:44958863..44960885-chr15:45018628..45021313,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B2M-1	chr15:45021199-45021750	NONHSAT042189

Variant related genes	Relation type
TRIM69	TF binding region
ENSG00000166710	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000229474	Chromatin interaction
ENSG00000165637	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1060392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295358	0.85[CEU][hapmap]
rs14711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901534	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1901535	0.81[ASN][1000 genomes]
rs1901537	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs2123149	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2254831	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2443976	0.86[EUR][1000 genomes]
rs2444003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2444009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2444010	0.87[EUR][1000 genomes]
rs2468064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2468071	0.83[YRI][hapmap]
rs2468074	0.88[EUR][1000 genomes]
rs2468075	0.86[EUR][1000 genomes]
rs2468077	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs2470911	0.96[YRI][hapmap]
rs2470914	0.88[EUR][1000 genomes]
rs3100139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3100142	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3110172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3110173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3110174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3110176	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3110182	0.87[EUR][1000 genomes]
rs3110662	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3110675	0.86[EUR][1000 genomes]
rs6493108	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493109	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs7168090	0.84[JPT][hapmap]
rs7172083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs935886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2290330	TRIM69	cis	Artery Tibial	GTEx
rs2290330	TRIM69	cis	Adipose Subcutaneous	GTEx
rs2290330	TRIM69	cis	Frontal Cortex	GTEx
rs2290330	TRIM69	cis	Muscle Skeletal	GTEx
rs2290330	TRIM69	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45019200-45021400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:45020200-45022400	Active TSS	Rectal Smooth Muscle	rectum
3	chr15:45020200-45023000	Active TSS	Brain Anterior Caudate	brain
4	chr15:45020400-45021400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:45020400-45021800	Active TSS	K562	blood
6	chr15:45020400-45022000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:45020400-45022000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:45020400-45022000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr15:45020400-45022000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr15:45020400-45022000	Active TSS	HepG2	liver
11	chr15:45020400-45022200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:45020400-45022400	Active TSS	A549	lung
13	chr15:45020400-45022400	Active TSS	HSMM	muscle
14	chr15:45020400-45022600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:45020400-45022800	Active TSS	Brain Germinal Matrix	brain
16	chr15:45020400-45022800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr15:45020400-45023600	Active TSS	GM12878-XiMat	blood
18	chr15:45020600-45021400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:45020600-45021600	Active TSS	Primary T cells from cord blood	blood
20	chr15:45020600-45021800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr15:45020600-45021800	Active TSS	Adipose Nuclei	Adipose
22	chr15:45020600-45021800	Active TSS	Fetal Lung	lung
23	chr15:45020600-45021800	Active TSS	Osteobl	bone
24	chr15:45020600-45022000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:45020600-45022000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:45020600-45022000	Active TSS	Liver	Liver
27	chr15:45020600-45022000	Active TSS	Esophagus	oesophagus
28	chr15:45020600-45022000	Active TSS	Fetal Intestine Large	intestine
29	chr15:45020600-45022000	Active TSS	Pancreas	Pancrea
30	chr15:45020600-45022000	Active TSS	Hela-S3	cervix
31	chr15:45020600-45022000	Active TSS	HSMMtube	muscle
32	chr15:45020600-45022200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr15:45020600-45022200	Active TSS	H9 Cell Line	embryonic stem cell
34	chr15:45020600-45022200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:45020600-45022200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr15:45020600-45022200	Active TSS	Brain Substantia Nigra	brain
37	chr15:45020600-45022200	Active TSS	Ovary	ovary
38	chr15:45020600-45022400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:45020600-45022400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr15:45020600-45022400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr15:45020600-45022400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:45020600-45022400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:45020600-45022400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:45020600-45022400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:45020600-45022400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:45020600-45022400	Active TSS	Colon Smooth Muscle	Colon
47	chr15:45020600-45022400	Active TSS	Fetal Stomach	stomach
48	chr15:45020600-45022400	Active TSS	Psoas Muscle	Psoas
49	chr15:45020600-45022400	Active TSS	HMEC	breast
50	chr15:45020600-45022600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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