Variant report

Variant	rs1516445
Chromosome Location	chr2:189762024-189762025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10737934	0.81[ASN][1000 genomes]
rs10737935	0.81[ASN][1000 genomes]
rs1155803	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13004114	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13009963	0.98[ASN][1000 genomes]
rs13010226	0.98[ASN][1000 genomes]
rs13010373	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013611	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400230	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516444	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516456	0.85[ASN][1000 genomes]
rs1543150	0.98[ASN][1000 genomes]
rs16830870	0.98[ASN][1000 genomes]
rs1829137	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1850275	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1850277	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1878203	0.97[ASN][1000 genomes]
rs1878205	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1914032	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996311	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1996312	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037188	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037189	0.81[ASN][1000 genomes]
rs2056157	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2067991	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2090357	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2459409	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708203	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4666766	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666767	0.99[ASN][1000 genomes]
rs4667253	0.80[ASN][1000 genomes]
rs6434301	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712676	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6734088	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7567967	0.97[ASN][1000 genomes]
rs7570793	0.81[ASN][1000 genomes]
rs7575426	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7607018	0.97[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	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1008847	chr2:189603961-189769705	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv875608	chr2:189753823-189837995	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189759600-189762200	Weak transcription	Fetal Stomach	stomach
2	chr2:189761400-189763200	Enhancers	Adipose Nuclei	Adipose
3	chr2:189761600-189762200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:189761600-189763000	Enhancers	Aorta	Aorta
5	chr2:189761800-189762200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:189761800-189762200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:189761800-189762200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:189761800-189762200	Flanking Active TSS	NHDF-Ad	bronchial
9	chr2:189761800-189762200	Flanking Active TSS	NHLF	lung
10	chr2:189761800-189762400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:189761800-189762600	Enhancers	Colon Smooth Muscle	Colon
12	chr2:189761800-189763000	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:189761800-189763000	Enhancers	Ovary	ovary
14	chr2:189761800-189763000	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:189761800-189763400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:189761800-189763400	Enhancers	Fetal Lung	lung
17	chr2:189761800-189763600	Enhancers	HSMM	muscle
18	chr2:189761800-189763800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:189762000-189762200	Enhancers	HSMMtube	muscle
20	chr2:189762000-189762400	Flanking Active TSS	Osteobl	bone
21	chr2:189762000-189762800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:189762000-189765400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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