Variant report

Variant	rs4489621
Chromosome Location	chr1:170279910-170279911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1034185	0.90[ASN][1000 genomes]
rs10494487	0.90[ASN][1000 genomes]
rs10919349	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919378	0.90[ASN][1000 genomes]
rs10919379	0.90[ASN][1000 genomes]
rs10919382	0.90[ASN][1000 genomes]
rs1113231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs11586686	0.90[ASN][1000 genomes]
rs12116910	1.00[CHB][hapmap]
rs12121358	0.90[ASN][1000 genomes]
rs12126109	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127149	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128082	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129359	0.90[ASN][1000 genomes]
rs12130105	0.90[ASN][1000 genomes]
rs12132288	0.90[ASN][1000 genomes]
rs12132402	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12135696	0.90[ASN][1000 genomes]
rs12137241	0.90[ASN][1000 genomes]
rs12138644	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139302	0.90[ASN][1000 genomes]
rs12141935	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12143611	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12407889	0.90[ASN][1000 genomes]
rs12408130	0.90[ASN][1000 genomes]
rs12732119	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12734846	0.90[ASN][1000 genomes]
rs12748912	0.90[ASN][1000 genomes]
rs12753359	0.90[ASN][1000 genomes]
rs1332963	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1332964	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1333142	1.00[CHB][hapmap]
rs1537390	1.00[CHB][hapmap]
rs17346122	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17346171	0.90[ASN][1000 genomes]
rs17350179	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17350305	0.82[ASN][1000 genomes]
rs1999523	1.00[CHB][hapmap]
rs2095135	0.90[ASN][1000 genomes]
rs28436845	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34161857	0.90[ASN][1000 genomes]
rs34860969	0.90[ASN][1000 genomes]
rs35084451	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35833908	0.90[ASN][1000 genomes]
rs4256872	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4300285	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4558042	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4575137	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4578264	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6657395	0.90[ASN][1000 genomes]
rs6667077	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684260	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6698352	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs7516510	0.90[ASN][1000 genomes]
rs7534693	0.90[ASN][1000 genomes]
rs7537355	0.90[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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4489621	SCYL3	cis	cerebellum	SCAN
rs4489621	C1orf156	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170276200-170280400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:170278200-170280400	Enhancers	Osteobl	bone
3	chr1:170278200-170280600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:170278400-170280000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:170278400-170280000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:170278400-170280200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:170278400-170280400	Enhancers	Fetal Muscle Leg	muscle
8	chr1:170278600-170280000	Enhancers	HSMMtube	muscle
9	chr1:170279000-170280000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:170279000-170280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:170279000-170280600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:170279000-170280600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:170279200-170284000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:170279400-170280200	Enhancers	NHLF	lung
15	chr1:170279400-170284000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:170279600-170281000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:170279800-170280000	Flanking Active TSS	NHDF-Ad	bronchial
18	chr1:170279800-170280200	Enhancers	NH-A	brain
19	chr1:170279800-170282600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:170279800-170284000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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