Variant report

Variant	rs58424833
Chromosome Location	chr1:91825439-91825440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10157861	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10493845	0.91[ASN][1000 genomes]
rs10801862	0.91[ASN][1000 genomes]
rs10923007	0.91[ASN][1000 genomes]
rs10923010	0.91[ASN][1000 genomes]
rs1158436	0.90[ASN][1000 genomes]
rs12093493	0.90[ASN][1000 genomes]
rs12562636	0.86[ASN][1000 genomes]
rs12564233	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566254	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566743	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568445	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568483	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs169472	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17131417	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17131419	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs182218	0.94[ASN][1000 genomes]
rs1823868	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs192519	0.81[ASN][1000 genomes]
rs281935	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281979	0.91[ASN][1000 genomes]
rs281992	0.91[ASN][1000 genomes]
rs281996	0.90[ASN][1000 genomes]
rs281998	0.91[ASN][1000 genomes]
rs282014	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282020	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs282050	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs282053	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34390075	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4084488	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4509624	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658202	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4658212	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658219	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4658220	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658221	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658222	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56738625	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59078007	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6671415	0.80[ASN][1000 genomes]
rs6685750	0.80[ASN][1000 genomes]
rs72726276	0.86[ASN][1000 genomes]
rs72970318	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72970328	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72970335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72970337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513687	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521314	0.91[ASN][1000 genomes]
rs876761	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9324372	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9660037	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9662393	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9724763	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs988203	0.88[EUR][1000 genomes];0.94[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1006022	chr1:91768640-91831196	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv871685	chr1:91774458-91849219	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs58424833	HFM1	cis	Artery Tibial	GTEx
rs58424833	HFM1	cis	Thyroid	GTEx
rs58424833	HFM1	cis	Muscle Skeletal	GTEx
rs58424833	HFM1	cis	lung	GTEx
rs58424833	HFM1	cis	Artery Aorta	GTEx
rs58424833	HFM1	cis	Adipose Subcutaneous	GTEx
rs58424833	HFM1	cis	Nerve Tibial	GTEx
rs58424833	HFM1	cis	Esophagus Muscularis	GTEx
rs58424833	HFM1	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91794000-91826600	Weak transcription	Fetal Heart	heart
2	chr1:91813400-91829600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:91818200-91831200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:91819400-91845200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:91820600-91842000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:91820800-91832000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:91821800-91832200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:91822600-91826000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:91822800-91825800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:91822800-91849000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:91823800-91825800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:91824200-91825600	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr1:91824200-91825600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr1:91824200-91825800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:91824200-91825800	ZNF genes & repeats	Fetal Brain Female	brain
16	chr1:91824200-91826000	ZNF genes & repeats	Ovary	ovary
17	chr1:91824200-91828800	Strong transcription	Fetal Lung	lung
18	chr1:91824600-91829600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:91824800-91827400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:91824800-91852600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:91825000-91827000	Weak transcription	Right Ventricle	heart
22	chr1:91825000-91829400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:91825000-91829400	Weak transcription	Fetal Kidney	kidney
24	chr1:91825000-91832200	Weak transcription	Fetal Stomach	stomach
25	chr1:91825000-91832200	Weak transcription	Pancreas	Pancrea
26	chr1:91825000-91852600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:91825400-91825800	Strong transcription	Left Ventricle	heart
28	chr1:91825400-91825800	ZNF genes & repeats	Psoas Muscle	Psoas

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