Variant report

Variant	rs4551620
Chromosome Location	chr1:57112106-57112107
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	chr1:57111495-57112171	Hela-S3	cervix:	n/a	n/a
2	TEAD4	chr1:57111577-57112168	H1-hESC	embryonic stem cell:	n/a	n/a
3	GTF2F1	chr1:57111414-57112145	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:57109759-57112147	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PPAP2B	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10749708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789036	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10789038	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789040	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10789041	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10889006	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889008	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889009	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11206884	0.90[ASN][1000 genomes]
rs11206885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206886	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206888	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206889	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206890	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206895	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1124900	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11589368	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11804779	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12021768	0.90[ASN][1000 genomes]
rs12021851	0.90[ASN][1000 genomes]
rs12023668	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12032999	0.88[ASN][1000 genomes]
rs12048572	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12072057	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12073311	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12078260	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12092267	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12097148	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12738355	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13374924	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1418442	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1986660	0.90[ASN][1000 genomes]
rs2245475	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2404718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404992	0.90[ASN][1000 genomes]
rs2404993	0.90[ASN][1000 genomes]
rs2404994	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2746345	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2746348	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2746349	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2746353	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2796517	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796519	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796523	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796527	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4548471	0.90[ASN][1000 genomes]
rs4562656	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4584419	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59223968	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772962	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61774287	0.90[ASN][1000 genomes]
rs6588641	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588643	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6683935	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72666470	0.86[ASN][1000 genomes]
rs7419053	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7515414	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7519509	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7533440	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7545066	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7546264	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7547486	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932447	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9887834	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9887940	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3402388	chr1:57109989-57112537	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3445991	chr1:57110114-57112162	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57109800-57112200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:57109800-57112200	Active TSS	Brain Angular Gyrus	brain
3	chr1:57109800-57112400	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:57109800-57113200	Active TSS	Right Atrium	heart
5	chr1:57109800-57114600	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:57110000-57112200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:57110000-57112200	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:57110000-57112200	Active TSS	Hela-S3	cervix
9	chr1:57110000-57112400	Active TSS	Brain Anterior Caudate	brain
10	chr1:57110000-57112400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:57110000-57112400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:57110000-57112600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:57110000-57113200	Active TSS	Stomach Smooth Muscle	stomach
14	chr1:57110000-57113400	Active TSS	Right Ventricle	heart
15	chr1:57110200-57112200	Active TSS	Aorta	Aorta
16	chr1:57110200-57112600	Active TSS	Left Ventricle	heart
17	chr1:57110200-57112600	Active TSS	A549	lung
18	chr1:57110200-57113000	Active TSS	Fetal Heart	heart
19	chr1:57110400-57112600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:57110600-57112400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr1:57111400-57112200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:57111400-57112200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:57111400-57112200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
24	chr1:57111400-57113000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:57111600-57112200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:57111600-57112200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr1:57111600-57112200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:57111600-57112200	Flanking Active TSS	Fetal Stomach	stomach
29	chr1:57111600-57112400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:57111800-57112200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr1:57111800-57112200	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr1:57111800-57112200	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr1:57111800-57112200	Flanking Active TSS	NHLF	lung
34	chr1:57111800-57112600	Active TSS	Fetal Muscle Trunk	muscle
35	chr1:57111800-57113000	Active TSS	Fetal Kidney	kidney
36	chr1:57111800-57113200	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:57112000-57112200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:57112000-57112200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:57112000-57112200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
40	chr1:57112000-57112200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:57112000-57112200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:57112000-57112200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:57112000-57112200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:57112000-57112200	Enhancers	Liver	Liver
45	chr1:57112000-57112200	Flanking Active TSS	Fetal Brain Female	brain
46	chr1:57112000-57112200	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr1:57112000-57112200	Bivalent/Poised TSS	NHDF-Ad	bronchial
48	chr1:57112000-57112400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:57112000-57112400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:57112000-57112400	Enhancers	Fetal Brain Male	brain

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