Variant report

Variant	rs57459746
Chromosome Location	chr3:139259212-139259213
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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:139257979-139259222	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1116748	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11549984	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489687	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493507	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391029	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391030	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391031	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511570	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511571	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337746	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397112	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011770	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772868	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3821543	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4270469	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407373	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683502	0.93[EUR][1000 genomes]
rs55641400	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642746	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724241	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780517	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55817881	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834130	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968289	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987999	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034427	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051054	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051514	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058641	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170893	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210757	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343214	0.92[EUR][1000 genomes]
rs73220932	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220940	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220941	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220944	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220945	0.97[ASN][1000 genomes]
rs893703	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs930412	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139257400-139259400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:139257600-139259400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:139257600-139259400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:139257600-139259400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:139257600-139259800	Active TSS	Ovary	ovary
6	chr3:139257800-139259400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:139257800-139259400	Active TSS	Brain Substantia Nigra	brain
8	chr3:139257800-139259400	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:139257800-139259400	Active TSS	Fetal Intestine Large	intestine
10	chr3:139257800-139259600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:139257800-139259600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:139257800-139259600	Active TSS	NH-A	brain
13	chr3:139257800-139259800	Active TSS	Pancreas	Pancrea
14	chr3:139257800-139259800	Active TSS	HSMMtube	muscle
15	chr3:139258000-139259400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr3:139258000-139259400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:139258000-139259400	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:139258000-139259600	Active TSS	Brain Anterior Caudate	brain
19	chr3:139258000-139259600	Active TSS	Fetal Stomach	stomach
20	chr3:139258200-139259400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:139258200-139259400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:139258200-139259400	Active TSS	Brain Hippocampus Middle	brain
23	chr3:139258200-139259800	Active TSS	Fetal Brain Female	brain
24	chr3:139258400-139259400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr3:139258400-139259400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr3:139258400-139259400	Active TSS	Fetal Brain Male	brain
27	chr3:139258400-139259400	Bivalent/Poised TSS	HepG2	liver
28	chr3:139258600-139259400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:139258600-139259400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:139258600-139259600	Active TSS	Right Atrium	heart
31	chr3:139258600-139259800	Weak transcription	Spleen	Spleen
32	chr3:139258800-139259600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr3:139258800-139260000	Active TSS	Fetal Muscle Trunk	muscle
34	chr3:139258800-139260000	Weak transcription	Lung	lung
35	chr3:139258800-139260200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr3:139259000-139259400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:139259000-139259400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr3:139259000-139259400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:139259000-139259600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:139259000-139259600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:139259000-139259600	Active TSS	Brain Germinal Matrix	brain
42	chr3:139259000-139259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:139259000-139259600	Enhancers	Fetal Heart	heart
44	chr3:139259000-139259800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:139259000-139259800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr3:139259000-139259800	Weak transcription	Right Ventricle	heart
47	chr3:139259000-139260000	Enhancers	HMEC	breast
48	chr3:139259000-139260200	Enhancers	Placenta	Placenta
49	chr3:139259000-139260400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr3:139259200-139259400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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