Variant report

Variant	rs60838770
Chromosome Location	chr21:40832556-40832557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40820022..40821902-chr21:40830927..40832560,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2063998	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2277787	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2410158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34145284	0.82[ASN][1000 genomes]
rs35286554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35360199	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71316676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71316677	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73367984	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73367987	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs60838770	LCA5L	cis	Thyroid	GTEx
rs60838770	SH3BGR	cis	Artery Tibial	GTEx
rs60838770	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs60838770	LCA5L	cis	Esophagus Mucosa	GTEx
rs60838770	LCA5L	cis	Artery Tibial	GTEx
rs60838770	LCA5L	cis	Nerve Tibial	GTEx
rs60838770	SH3BGR	cis	Thyroid	GTEx
rs60838770	LCA5L	cis	Artery Aorta	GTEx
rs60838770	LCA5L	cis	Esophagus Muscularis	GTEx
rs60838770	LCA5L	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
2	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr21:40825600-40836800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr21:40826600-40849800	Weak transcription	HSMMtube	muscle
5	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:40827800-40835200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr21:40828200-40839600	Weak transcription	Fetal Muscle Leg	muscle
8	chr21:40828400-40835400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr21:40828600-40835400	Weak transcription	Left Ventricle	heart
10	chr21:40828600-40835600	Weak transcription	Brain Hippocampus Middle	brain
11	chr21:40828600-40847400	Weak transcription	Brain Substantia Nigra	brain
12	chr21:40828800-40834600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr21:40828800-40834800	Weak transcription	Right Ventricle	heart
14	chr21:40828800-40835400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:40828800-40847600	Weak transcription	Brain Angular Gyrus	brain
16	chr21:40828800-40847600	Weak transcription	Brain Anterior Caudate	brain
17	chr21:40829800-40834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr21:40829800-40856200	Weak transcription	Aorta	Aorta
19	chr21:40830000-40835600	Weak transcription	Fetal Heart	heart
20	chr21:40830200-40849800	Weak transcription	Primary T cells from cord blood	blood
21	chr21:40832200-40839600	Weak transcription	Psoas Muscle	Psoas

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