Variant report

Variant	rs2692623
Chromosome Location	chr3:119317279-119317280
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	RCOR1	chr3:119316992-119318319	GM12878	blood:	n/a	n/a
3	BCL11A	chr3:119316773-119317613	GM12878	blood:	n/a	n/a
4	RELA	chr3:119316319-119318154	GM18505	blood:	n/a	n/a
5	POLR2A	chr3:119317249-119318242	GM12891	blood:	n/a	n/a
6	POU2F2	chr3:119317073-119317620	GM12878	blood:	n/a	chr3:119317351-119317364 chr3:119317354-119317365 chr3:119317351-119317366 chr3:119317354-119317363 chr3:119317354-119317364 chr3:119317355-119317362 chr3:119317352-119317366 chr3:119317350-119317368
7	POLR2A	chr3:119315795-119320559	GM12878	blood:	n/a	n/a
8	ZNF143	chr3:119316507-119317762	GM12878	blood:	n/a	chr3:119316529-119316548 chr3:119316530-119316545
9	RELA	chr3:119316639-119318712	GM12891	blood:	n/a	n/a
10	TCF12	chr3:119317217-119317618	GM12878	blood:	n/a	n/a
11	MAZ	chr3:119316404-119317894	GM12878	blood:	n/a	chr3:119316669-119316679
12	TCF12	chr3:119317196-119317489	GM12878	blood:	n/a	n/a
13	EBF1	chr3:119316230-119320348	GM12878	blood:	n/a	chr3:119317324-119317335
14	IKZF1	chr3:119316165-119317802	GM12878	blood:	n/a	n/a
15	RELA	chr3:119316499-119317851	GM18526	blood:	n/a	n/a
16	POLR2A	chr3:119316322-119320295	GM12891	blood:	n/a	n/a
17	STAT5A	chr3:119317078-119319327	GM12878	blood:	n/a	chr3:119318677-119318689 chr3:119319078-119319086
18	RELA	chr3:119316349-119317809	GM12878	blood:	n/a	n/a
19	ATF2	chr3:119316171-119318970	GM12878	blood:	n/a	n/a
20	MEF2A	chr3:119316677-119317628	GM12878	blood:	n/a	n/a
21	STAT3	chr3:119316180-119317854	GM12878	blood:	n/a	chr3:119316548-119316559
22	NFIC	chr3:119315804-119319171	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:119317245-119320053	GM12892	blood:	n/a	n/a
24	MXI1	chr3:119317263-119317875	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:119316342-119320274	GM18951	blood:	n/a	n/a
26	RELA	chr3:119316328-119318748	GM18951	blood:	n/a	n/a
27	RELA	chr3:119316350-119318741	GM15510	blood:	n/a	n/a
28	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
29	POU2F2	chr3:119317166-119317554	GM12878	blood:	n/a	chr3:119317351-119317364 chr3:119317354-119317365 chr3:119317351-119317366 chr3:119317354-119317363 chr3:119317354-119317364 chr3:119317355-119317362 chr3:119317352-119317366 chr3:119317350-119317368
30	NFIC	chr3:119316248-119317727	GM12878	blood:	n/a	n/a
31	STAT5A	chr3:119317184-119318032	GM12878	blood:	n/a	n/a
32	SP1	chr3:119317076-119317667	GM12878	blood:	n/a	n/a
33	BCLAF1	chr3:119317146-119317826	GM12878	blood:	n/a	n/a
34	CEBPB	chr3:119316601-119318949	GM12878	blood:	n/a	chr3:119317085-119317098
35	POLR2A	chr3:119317212-119319940	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr3:119316352-119317863	GM12878	blood:	n/a	n/a
37	SMC3	chr3:119316523-119318090	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:119317138-119320307	GM12892	blood:	n/a	n/a
39	PML	chr3:119317241-119317595	GM12878	blood:	n/a	n/a
40	RELA	chr3:119316289-119318031	GM12892	blood:	n/a	n/a
41	CHD2	chr3:119316648-119319935	GM12878	blood:	n/a	n/a
42	EP300	chr3:119316305-119317951	GM12878	blood:	n/a	n/a
43	WRNIP1	chr3:119317226-119320130	GM12878	blood:	n/a	n/a
44	EP300	chr3:119316239-119317922	GM12878	blood:	n/a	n/a
45	CHD1	chr3:119316263-119320189	GM12878	blood:	n/a	n/a
46	FOXM1	chr3:119316168-119317781	GM12878	blood:	n/a	n/a
47	BATF	chr3:119317199-119317631	GM12878	blood:	n/a	n/a
48	BCLAF1	chr3:119316211-119318576	GM12878	blood:	n/a	chr3:119318543-119318552
49	RELA	chr3:119316313-119319077	GM19099	blood:	n/a	n/a
50	EBF1	chr3:119316867-119317598	GM12878	blood:	n/a	chr3:119317324-119317335

Variant related genes	Relation type
PLA1A	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10433338	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13443	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525838	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534154	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723969	0.96[ASN][1000 genomes]
rs1797831	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797832	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049501	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171025	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248483	0.96[ASN][1000 genomes]
rs2251566	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272267	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272268	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272269	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272270	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629399	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629400	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629408	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670293	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670298	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688637	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688638	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688639	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688646	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688647	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688648	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692612	0.96[ASN][1000 genomes]
rs2692613	0.94[ASN][1000 genomes]
rs2692614	0.96[ASN][1000 genomes]
rs2692615	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692621	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474926	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485257	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487124	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528765	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530389	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530783	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536624	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538136	0.97[ASN][1000 genomes]
rs551885	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555525	1.00[ASN][1000 genomes]
rs55670246	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801535	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197198	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58020513	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593968	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666134	0.95[ASN][1000 genomes]
rs6807201	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807613	0.94[ASN][1000 genomes]
rs72954966	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:38 , 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	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:119314800-119317400	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:119315000-119317800	Enhancers	Adipose Nuclei	Adipose
7	chr3:119315000-119318000	Enhancers	Psoas Muscle	Psoas
8	chr3:119315000-119320200	Enhancers	Left Ventricle	heart
9	chr3:119315200-119317400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:119315400-119317600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:119315400-119319200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:119315600-119317800	Weak transcription	Gastric	stomach
13	chr3:119315600-119319000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:119315600-119319600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:119316000-119317400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119316000-119319200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:119316200-119318200	Enhancers	Fetal Kidney	kidney
18	chr3:119316200-119319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:119316200-119319400	Weak transcription	Placenta	Placenta
20	chr3:119316200-119319600	Weak transcription	Spleen	Spleen
21	chr3:119316200-119340600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:119316400-119317400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:119316400-119318200	Flanking Active TSS	Liver	Liver
24	chr3:119316400-119320600	Flanking Active TSS	GM12878-XiMat	blood
25	chr3:119316600-119317800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:119316600-119320200	Enhancers	Right Ventricle	heart
27	chr3:119316800-119317600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:119317000-119317400	Weak transcription	Ovary	ovary
29	chr3:119317000-119317400	Weak transcription	Pancreas	Pancrea
30	chr3:119317000-119317600	Enhancers	Fetal Intestine Small	intestine
31	chr3:119317000-119319000	Enhancers	Fetal Intestine Large	intestine
32	chr3:119317000-119319800	Weak transcription	Fetal Lung	lung
33	chr3:119317000-119319800	Weak transcription	HepG2	liver
34	chr3:119317000-119323800	Weak transcription	HSMMtube	muscle
35	chr3:119317200-119317400	Weak transcription	Lung	lung
36	chr3:119317200-119317600	Enhancers	Duodenum Mucosa	Duodenum
37	chr3:119317200-119320200	Enhancers	Right Atrium	heart
38	chr3:119317200-119321200	Weak transcription	HUVEC	blood vessel

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