Variant report

Variant	rs12089958
Chromosome Location	chr1:221001363-221001364
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	CTCF	chr1:221001345-221001375	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000238078	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10495152	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863567	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863568	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118609	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118611	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118615	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118616	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118619	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590678	0.83[ASN][1000 genomes]
rs12057411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073837	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117818	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124030	0.83[ASN][1000 genomes]
rs12129004	0.82[EUR][1000 genomes]
rs12139139	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145674	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335919	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1494368	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494371	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1494372	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17008806	0.83[ASN][1000 genomes]
rs17596850	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17650107	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279638	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378425	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35730037	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4143773	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61830270	0.88[ASN][1000 genomes]
rs61830289	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6541161	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668666	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673877	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693017	0.87[ASN][1000 genomes]
rs7530074	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530493	0.97[ASN][1000 genomes]
rs7544735	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553447	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881995	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903319	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs984676	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220980400-221001400	Weak transcription	Gastric	stomach
2	chr1:220984200-221001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:220984600-221006600	Weak transcription	Psoas Muscle	Psoas
4	chr1:220987600-221003800	Weak transcription	HepG2	liver
5	chr1:220992000-221002600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:220995600-221005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:220996000-221001400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:220997400-221003400	Enhancers	Liver	Liver
9	chr1:220998000-221001600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:220998200-221001600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:220998200-221004200	Weak transcription	Aorta	Aorta
12	chr1:220999200-221002800	Enhancers	Fetal Lung	lung
13	chr1:220999200-221003600	Enhancers	Fetal Heart	heart
14	chr1:220999600-221001800	Enhancers	Lung	lung
15	chr1:220999800-221001400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:220999800-221002200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:220999800-221002600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:221000000-221001400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:221000000-221002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:221000200-221001800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:221000400-221001600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:221000800-221001400	Enhancers	HUVEC	blood vessel
23	chr1:221000800-221001600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:221000800-221001600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:221000800-221001600	Enhancers	Stomach Mucosa	stomach
26	chr1:221000800-221001800	Enhancers	Spleen	Spleen
27	chr1:221000800-221002000	Enhancers	Fetal Intestine Small	intestine
28	chr1:221000800-221002600	Enhancers	Fetal Intestine Large	intestine
29	chr1:221000800-221002800	Enhancers	Right Ventricle	heart
30	chr1:221001000-221001400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:221001000-221001400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:221001000-221001600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:221001000-221001800	Bivalent Enhancer	Fetal Stomach	stomach
34	chr1:221001000-221001800	Enhancers	Ovary	ovary
35	chr1:221001000-221003400	Enhancers	Left Ventricle	heart
36	chr1:221001000-221004200	Enhancers	Right Atrium	heart
37	chr1:221001000-221004800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:221001200-221001600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:221001200-221001600	Enhancers	Placenta	Placenta
40	chr1:221001200-221001800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:221001200-221001800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:221001200-221002000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:221001200-221002800	Enhancers	Adipose Nuclei	Adipose
44	chr1:221001200-221003200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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