Variant report

Variant	rs558939339
Chromosome Location	chr3:119316991-119316992
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	TBP	chr3:119316323-119317977	GM12878	blood:	n/a	n/a
2	BCL11A	chr3:119316773-119317613	GM12878	blood:	n/a	n/a
3	RELA	chr3:119316319-119318154	GM18505	blood:	n/a	n/a
4	MTA3	chr3:119315827-119317029	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:119315795-119320559	GM12878	blood:	n/a	n/a
6	ZNF143	chr3:119316507-119317762	GM12878	blood:	n/a	chr3:119316529-119316548 chr3:119316530-119316545
7	RELA	chr3:119316639-119318712	GM12891	blood:	n/a	n/a
8	MAZ	chr3:119316404-119317894	GM12878	blood:	n/a	chr3:119316669-119316679
9	EBF1	chr3:119316230-119320348	GM12878	blood:	n/a	chr3:119317324-119317335
10	IKZF1	chr3:119316165-119317802	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:119316160-119317039	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:119316055-119317070	GM12892	blood:	n/a	n/a
13	RELA	chr3:119316499-119317851	GM18526	blood:	n/a	n/a
14	POLR2A	chr3:119316322-119320295	GM12891	blood:	n/a	n/a
15	RELA	chr3:119316349-119317809	GM12878	blood:	n/a	n/a
16	ATF2	chr3:119316171-119318970	GM12878	blood:	n/a	n/a
17	MEF2A	chr3:119316677-119317628	GM12878	blood:	n/a	n/a
18	STAT3	chr3:119316180-119317854	GM12878	blood:	n/a	chr3:119316548-119316559
19	NFIC	chr3:119315804-119319171	GM12878	blood:	n/a	n/a
20	ZNF384	chr3:119316885-119317130	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:119316342-119320274	GM18951	blood:	n/a	n/a
22	RELA	chr3:119316328-119318748	GM18951	blood:	n/a	n/a
23	RELA	chr3:119316350-119318741	GM15510	blood:	n/a	n/a
24	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
25	NFIC	chr3:119316248-119317727	GM12878	blood:	n/a	n/a
26	CEBPB	chr3:119316601-119318949	GM12878	blood:	n/a	chr3:119317085-119317098
27	STAT5A	chr3:119316685-119317173	GM12878	blood:	n/a	n/a
28	TBL1XR1	chr3:119316352-119317863	GM12878	blood:	n/a	n/a
29	SMC3	chr3:119316523-119318090	GM12878	blood:	n/a	n/a
30	RELA	chr3:119316289-119318031	GM12892	blood:	n/a	n/a
31	CHD2	chr3:119316648-119319935	GM12878	blood:	n/a	n/a
32	EP300	chr3:119316305-119317951	GM12878	blood:	n/a	n/a
33	EP300	chr3:119316239-119317922	GM12878	blood:	n/a	n/a
34	CHD1	chr3:119316263-119320189	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:119315803-119317101	GM12892	blood:	n/a	n/a
36	FOXM1	chr3:119316168-119317781	GM12878	blood:	n/a	n/a
37	BCLAF1	chr3:119316211-119318576	GM12878	blood:	n/a	chr3:119318543-119318552
38	RELA	chr3:119316313-119319077	GM19099	blood:	n/a	n/a
39	EBF1	chr3:119316867-119317598	GM12878	blood:	n/a	chr3:119317324-119317335
40	RUNX3	chr3:119315732-119318846	GM12878	blood:	n/a	chr3:119316012-119316021 chr3:119316012-119316021
41	MEF2A	chr3:119316713-119317553	GM12878	blood:	n/a	n/a
42	EP300	chr3:119316646-119317499	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a
44	BHLHE40	chr3:119316293-119317958	GM12878	blood:	n/a	n/a
45	RUNX3	chr3:119316274-119318129	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:119315801-119317086	GM12892	blood:	n/a	n/a
47	CUX1	chr3:119316413-119318898	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:119315907-119320520	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:119316217-119320450	GM12878	blood:	n/a	n/a
50	MTA3	chr3:119315715-119320461	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PLA1A	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv591363	chr3:119316828-119345950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
2	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119314200-119317200	Enhancers	Lung	lung
5	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119314800-119317400	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:119315000-119317800	Enhancers	Adipose Nuclei	Adipose
8	chr3:119315000-119318000	Enhancers	Psoas Muscle	Psoas
9	chr3:119315000-119320200	Enhancers	Left Ventricle	heart
10	chr3:119315200-119317000	Enhancers	A549	lung
11	chr3:119315200-119317000	Enhancers	HepG2	liver
12	chr3:119315200-119317000	Enhancers	HSMMtube	muscle
13	chr3:119315200-119317400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:119315400-119317600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:119315400-119319200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:119315600-119317800	Weak transcription	Gastric	stomach
17	chr3:119315600-119319000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:119315600-119319600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:119316000-119317200	Enhancers	HUVEC	blood vessel
20	chr3:119316000-119317400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:119316000-119319200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:119316200-119317000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:119316200-119317000	Enhancers	Stomach Mucosa	stomach
24	chr3:119316200-119317200	Weak transcription	Right Atrium	heart
25	chr3:119316200-119318200	Enhancers	Fetal Kidney	kidney
26	chr3:119316200-119319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:119316200-119319400	Weak transcription	Placenta	Placenta
28	chr3:119316200-119319600	Weak transcription	Spleen	Spleen
29	chr3:119316200-119340600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:119316400-119317400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr3:119316400-119318200	Flanking Active TSS	Liver	Liver
32	chr3:119316400-119320600	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:119316600-119317000	Enhancers	Osteobl	bone
34	chr3:119316600-119317800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:119316600-119320200	Enhancers	Right Ventricle	heart
36	chr3:119316800-119317000	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr3:119316800-119317000	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr3:119316800-119317000	Enhancers	Fetal Lung	lung
39	chr3:119316800-119317000	Enhancers	Ovary	ovary
40	chr3:119316800-119317000	Enhancers	Pancreas	Pancrea
41	chr3:119316800-119317000	Enhancers	Small Intestine	intestine
42	chr3:119316800-119317200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:119316800-119317600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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