Variant report

Variant	rs10485898
Chromosome Location	chr7:78105184-78105185
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10241266	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10257012	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11763843	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12705479	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12705480	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1990579	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6466241	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6466242	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6651114	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7794954	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7806044	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7808641	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9691175	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9886106	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10485898	UPK3B	cis	cerebellum	SCAN
rs10485898	CCDC146	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78099800-78106200	Weak transcription	Brain Angular Gyrus	brain
2	chr7:78101800-78105600	Enhancers	Brain Anterior Caudate	brain
3	chr7:78102200-78108200	Weak transcription	Ovary	ovary
4	chr7:78102600-78106400	Weak transcription	HSMMtube	muscle
5	chr7:78103000-78117600	Weak transcription	Fetal Brain Female	brain
6	chr7:78103200-78105800	Weak transcription	HSMM	muscle
7	chr7:78103200-78106000	Weak transcription	Brain Substantia Nigra	brain
8	chr7:78103400-78105400	Weak transcription	Osteobl	bone
9	chr7:78103400-78108600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:78103400-78108600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:78103600-78105400	Enhancers	Fetal Heart	heart
12	chr7:78103800-78115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:78104400-78105600	Enhancers	Brain Hippocampus Middle	brain
14	chr7:78104400-78106600	Enhancers	Brain Cingulate Gyrus	brain
15	chr7:78104400-78116800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:78105000-78105200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:78105000-78106600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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