Variant report

Variant	rs35360199
Chromosome Location	chr21:40835823-40835824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40832121..40834970-chr21:40835778..40838061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185437	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34564680	0.82[ASN][1000 genomes]
rs34664105	0.82[ASN][1000 genomes]
rs35286554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35643585	0.82[ASN][1000 genomes]
rs35668465	0.82[ASN][1000 genomes]
rs60838770	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71316676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316678	0.82[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
rs35360199	SH3BGR	cis	Artery Tibial	GTEx
rs35360199	LCA5L	cis	Thyroid	GTEx
rs35360199	LCA5L	cis	Artery Tibial	GTEx
rs35360199	LCA5L	cis	Nerve Tibial	GTEx
rs35360199	LCA5L	cis	Esophagus Muscularis	GTEx
rs35360199	LCA5L	cis	Esophagus Mucosa	GTEx
rs35360199	LCA5L	cis	Artery Aorta	GTEx
rs35360199	SH3BGR	cis	Thyroid	GTEx
rs35360199	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs35360199	LCA5L	cis	lung	GTEx

Chromatin state (count:24 , 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	chr21:40828200-40839600	Weak transcription	Fetal Muscle Leg	muscle
7	chr21:40828600-40847400	Weak transcription	Brain Substantia Nigra	brain
8	chr21:40828800-40847600	Weak transcription	Brain Angular Gyrus	brain
9	chr21:40828800-40847600	Weak transcription	Brain Anterior Caudate	brain
10	chr21:40829800-40856200	Weak transcription	Aorta	Aorta
11	chr21:40830200-40849800	Weak transcription	Primary T cells from cord blood	blood
12	chr21:40832200-40839600	Weak transcription	Psoas Muscle	Psoas
13	chr21:40833000-40847200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr21:40834200-40837600	Weak transcription	Liver	Liver
15	chr21:40834600-40836600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr21:40834800-40836400	Strong transcription	Right Ventricle	heart
17	chr21:40835200-40836200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr21:40835400-40836200	Strong transcription	Brain Cingulate Gyrus	brain
19	chr21:40835400-40836800	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr21:40835400-40840600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:40835600-40836400	Strong transcription	Brain Hippocampus Middle	brain
22	chr21:40835600-40851000	Weak transcription	Ovary	ovary
23	chr21:40835800-40836000	Genic enhancers	Fetal Heart	heart
24	chr21:40835800-40847800	Weak transcription	Left Ventricle	heart

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