Variant report

Variant	rs1816391
Chromosome Location	chr5:57121242-57121243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12519846	0.99[ASN][1000 genomes]
rs1347072	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1347073	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1432477	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1432480	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1432481	0.83[ASN][1000 genomes]
rs1835873	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1835875	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1835876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053013	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215813	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2539732	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2539734	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2568533	0.84[ASN][1000 genomes]
rs2568534	0.83[ASN][1000 genomes]
rs2568535	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2568536	0.83[ASN][1000 genomes]
rs2898030	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898032	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34152283	0.85[ASN][1000 genomes]
rs34711481	0.89[ASN][1000 genomes]
rs35483666	1.00[ASN][1000 genomes]
rs4700229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62360111	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6450440	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6450441	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6892809	0.99[ASN][1000 genomes]
rs757635	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7701201	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs854025	0.84[ASN][1000 genomes]
rs854026	0.84[ASN][1000 genomes]
rs854027	0.84[ASN][1000 genomes]
rs854030	0.84[ASN][1000 genomes]
rs854032	0.84[ASN][1000 genomes]
rs854034	0.84[ASN][1000 genomes]
rs887868	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs988658	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]

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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1816391	IL6ST	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57118000-57122600	Enhancers	HMEC	breast
2	chr5:57118600-57121600	Enhancers	NHLF	lung
3	chr5:57118600-57122400	Enhancers	HSMM	muscle
4	chr5:57118600-57122600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:57118600-57122600	Enhancers	NHEK	skin
6	chr5:57119200-57121800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:57119200-57121800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:57119400-57121600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:57119400-57121600	Enhancers	NHDF-Ad	bronchial
10	chr5:57119400-57121800	Enhancers	Osteobl	bone
11	chr5:57119400-57122000	Enhancers	Hela-S3	cervix
12	chr5:57119600-57121400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:57119600-57121800	Enhancers	HSMMtube	muscle
14	chr5:57120000-57121800	Enhancers	A549	lung
15	chr5:57120600-57121400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr5:57120600-57121400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:57120600-57121600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr5:57120600-57121800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:57120600-57121800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:57120600-57122000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:57120600-57123000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:57120800-57121800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:57121000-57121400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr5:57121000-57121800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:57121000-57121800	Enhancers	NH-A	brain
26	chr5:57121000-57122200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:57121200-57121600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:57121200-57121600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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