Variant report

Variant	rs72954966
Chromosome Location	chr3:119314783-119314784
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	MTA3	chr3:119314705-119315717	GM12878	blood:	n/a	n/a
2	ARID3A	chr3:119314488-119314801	HepG2	liver:	n/a	n/a
3	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
4	PRDM1	chr3:119314715-119314915	Hela-S3	cervix:	n/a	chr3:119314853-119314867 chr3:119314853-119314866 chr3:119314857-119314866 chr3:119314852-119314867
5	POLR2A	chr3:119314781-119315682	GM12891	blood:	n/a	n/a
6	EBF1	chr3:119314713-119315143	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119314543..119316146-chr3:119316320..119318446,2	K562	blood:
2	chr3:119310790..119313134-chr3:119314484..119316186,2	K562	blood:

Variant related genes	Relation type
PLA1A	TF binding region
ENSG00000144837	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10433338	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525838	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534154	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723969	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797831	0.96[ASN][1000 genomes]
rs1797832	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20569	0.80[EUR][1000 genomes]
rs2171025	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248483	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251566	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272267	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272268	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272269	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272270	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629399	0.96[ASN][1000 genomes]
rs2629400	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629408	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670293	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670298	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688637	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688638	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688639	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688646	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688647	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688648	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692612	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692613	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692614	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692615	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692623	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474926	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485257	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528765	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530389	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536624	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538136	0.97[ASN][1000 genomes]
rs551885	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555525	1.00[ASN][1000 genomes]
rs55670246	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801535	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197198	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58020513	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666134	0.95[ASN][1000 genomes]
rs6807201	0.96[ASN][1000 genomes]
rs6807613	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299200-119315000	Weak transcription	Gastric	stomach
2	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
3	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
4	chr3:119307600-119316400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:119308200-119314800	Weak transcription	Aorta	Aorta
6	chr3:119309800-119314800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:119311000-119315000	Weak transcription	Spleen	Spleen
9	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:119311200-119316800	Weak transcription	Fetal Lung	lung
11	chr3:119313000-119314800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:119313400-119314800	Weak transcription	Placenta	Placenta
13	chr3:119314200-119315400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr3:119314200-119315600	Enhancers	Right Ventricle	heart
15	chr3:119314200-119315600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr3:119314200-119317200	Enhancers	Lung	lung
17	chr3:119314400-119314800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr3:119314400-119314800	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr3:119314400-119315000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr3:119314400-119315000	Flanking Active TSS	HSMM	muscle
21	chr3:119314400-119315200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:119314400-119315200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:119314400-119315200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:119314400-119315200	Flanking Active TSS	HSMMtube	muscle
25	chr3:119314400-119315400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:119314400-119315600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:119314600-119314800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:119314600-119314800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:119314600-119314800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:119314600-119314800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:119314600-119314800	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr3:119314600-119314800	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr3:119314600-119314800	Active TSS	Ovary	ovary
35	chr3:119314600-119314800	Flanking Bivalent TSS/Enh	HepG2	liver
36	chr3:119314600-119314800	Active TSS	NHDF-Ad	bronchial
37	chr3:119314600-119315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:119314600-119315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:119314600-119315000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:119314600-119315000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:119314600-119315000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:119314600-119315000	Flanking Active TSS	Liver	Liver
43	chr3:119314600-119315000	Enhancers	Brain Germinal Matrix	brain
44	chr3:119314600-119315000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:119314600-119315000	Active TSS	Colonic Mucosa	Colon
46	chr3:119314600-119315000	Enhancers	Fetal Muscle Trunk	muscle
47	chr3:119314600-119315000	Flanking Active TSS	Left Ventricle	heart
48	chr3:119314600-119315000	Flanking Active TSS	Psoas Muscle	Psoas
49	chr3:119314600-119315000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:119314600-119315000	Flanking Active TSS	Right Atrium	heart

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