Variant report

Variant	rs3184088
Chromosome Location	chr15:74890354-74890355
allele	A/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	PML	chr15:74890334-74891405	GM12878	blood:	n/a	chr15:74890670-74890678
2	USF1	chr15:74890313-74891222	SK-N-SH	brain:	n/a	chr15:74890756-74890765 chr15:74890757-74890766 chr15:74890758-74890767 chr15:74890757-74890766 chr15:74890751-74890772
3	NFYB	chr15:74890339-74891361	K562	blood:	n/a	chr15:74890769-74890784 chr15:74890772-74890787 chr15:74890740-74890752 chr15:74890772-74890787 chr15:74890738-74890753
4	POLR2A	chr15:74890313-74891438	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:74889246-74891561	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:74890339-74892306	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:74889778-74890393	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr15:74890278-74891225	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:74889190-74891407	GM12891	blood:	n/a	n/a
10	NR2F2	chr15:74890331-74891251	K562	blood:	n/a	n/a
11	SP1	chr15:74890350-74891232	HCT-116	colon:	n/a	chr15:74891078-74891087 chr15:74890773-74890794 chr15:74891076-74891088 chr15:74891077-74891086 chr15:74890729-74890750 chr15:74891078-74891087 chr15:74890786-74890800 chr15:74890791-74890800 chr15:74891076-74891088
12	POLR2A	chr15:74889524-74891603	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:74889245-74890437	GM12878	blood:	n/a	n/a
14	USF1	chr15:74890351-74891100	ECC-1	luminal epithelium:	n/a	chr15:74890756-74890765 chr15:74890757-74890766 chr15:74890758-74890767 chr15:74890757-74890766 chr15:74890751-74890772
15	NR2F2	chr15:74890316-74891169	K562	blood:	n/a	n/a
16	RFX5	chr15:74890306-74891749	IMR90	lung:	n/a	chr15:74890775-74890784 chr15:74890887-74890901
17	POLR2A	chr15:74889335-74891434	GM12892	blood:	n/a	n/a
18	USF1	chr15:74890318-74891233	HCT-116	colon:	n/a	chr15:74890756-74890765 chr15:74890757-74890766 chr15:74890758-74890767 chr15:74890757-74890766 chr15:74890751-74890772
19	RFX5	chr15:74890239-74891640	SK-N-SH	brain:	n/a	chr15:74890775-74890784 chr15:74890887-74890901
20	POLR2A	chr15:74890282-74892472	K562	blood:	n/a	n/a
21	POLR2A	chr15:74889186-74892383	GM12878	blood:	n/a	n/a
22	EP300	chr15:74890348-74891761	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr15:74890345-74891468	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr15:74890151-74891218	GM12891	blood:	n/a	n/a
25	POLR2A	chr15:74889679-74892784	K562	blood:	n/a	n/a
26	POLR2A	chr15:74890313-74891259	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr15:74890352-74891409	GM12891	blood:	n/a	n/a
28	MTA3	chr15:74890339-74891509	GM12878	blood:	n/a	n/a
29	RXRA	chr15:74890297-74891328	SK-N-SH	brain:	n/a	chr15:74890566-74890582
30	MTA3	chr15:74890309-74891864	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:74890008-74891468	GM12878	blood:	n/a	n/a
32	MXI1	chr15:74890254-74891521	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr15:74890217-74893806	PBDE	blood:	n/a	n/a
34	RUNX3	chr15:74890331-74891484	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:74889224-74891494	GM12892	blood:	n/a	n/a
36	POLR2A	chr15:74890235-74891863	HepG2	liver:	n/a	n/a
37	POLR2A	chr15:74890178-74891255	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74885278..74889186-chr15:74890286..74893326,4	K562	blood:
2	chr15:74885692..74889192-chr15:74889315..74893477,4	MCF-7	breast:

Variant related genes	Relation type
CLK3	TF binding region
ENSG00000179361	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12591497	0.81[AMR][1000 genomes]
rs12593898	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12594105	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12594316	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12594462	1.00[CEU][hapmap]
rs16953854	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16969770	1.00[CEU][hapmap]
rs1799814	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3747478	1.00[CEU][hapmap]
rs58386058	0.81[EUR][1000 genomes]
rs58747223	0.81[EUR][1000 genomes]
rs60494023	0.88[AMR][1000 genomes]
rs8023274	1.00[CEU][hapmap]
rs8031284	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv976950	chr15:74888247-74891372	Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv817698	chr15:74889163-75019449	Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74840600-74890400	Weak transcription	Stomach Mucosa	stomach
2	chr15:74845800-74890400	Weak transcription	A549	lung
3	chr15:74863600-74890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:74863800-74890400	Weak transcription	Psoas Muscle	Psoas
5	chr15:74866800-74890800	Weak transcription	Ovary	ovary
6	chr15:74877400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:74881000-74890400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:74881200-74890400	Weak transcription	Fetal Kidney	kidney
9	chr15:74881200-74892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:74881400-74890400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:74881400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:74881400-74890400	Weak transcription	Fetal Brain Male	brain
13	chr15:74881400-74892200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:74881600-74890400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:74881800-74890400	Weak transcription	HSMM	muscle
16	chr15:74882000-74890800	Weak transcription	Right Atrium	heart
17	chr15:74882200-74890400	Weak transcription	NH-A	brain
18	chr15:74882600-74890400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:74882600-74890400	Weak transcription	NHDF-Ad	bronchial
20	chr15:74883200-74890400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:74883400-74890400	Weak transcription	HUVEC	blood vessel
22	chr15:74883400-74892000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:74883600-74890800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:74884600-74890400	Weak transcription	Small Intestine	intestine
25	chr15:74884800-74890400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:74884800-74890400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:74884800-74890400	Strong transcription	Placenta	Placenta
28	chr15:74884800-74890800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:74885000-74890400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:74885200-74890400	Weak transcription	Pancreas	Pancrea
31	chr15:74885200-74890400	Weak transcription	HSMMtube	muscle
32	chr15:74885600-74890400	Weak transcription	Left Ventricle	heart
33	chr15:74885600-74890400	Weak transcription	NHEK	skin
34	chr15:74885600-74890400	Weak transcription	NHLF	lung
35	chr15:74885600-74890800	Weak transcription	Right Ventricle	heart
36	chr15:74885800-74890400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:74885800-74890400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:74886000-74890400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:74886000-74890400	Weak transcription	Brain Angular Gyrus	brain
40	chr15:74886000-74890400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:74886000-74890400	Weak transcription	Osteobl	bone
42	chr15:74886000-74890600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:74886000-74891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:74886200-74890400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:74886200-74890400	Weak transcription	Fetal Lung	lung
46	chr15:74886400-74890400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:74886600-74890400	Weak transcription	Thymus	Thymus
48	chr15:74887200-74890400	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:74887200-74890400	Weak transcription	Colonic Mucosa	Colon
50	chr15:74887200-74890400	Weak transcription	Rectal Smooth Muscle	rectum

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