Variant report

Variant	rs10514880
Chromosome Location	chr5:59112854-59112855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1003218	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1003219	0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10042020	0.92[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10066777	0.89[ASN][1000 genomes]
rs10514888	0.93[GIH][hapmap]
rs13171758	0.84[EUR][1000 genomes]
rs13186506	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs13189631	0.92[EUR][1000 genomes]
rs1369286	0.93[ASN][1000 genomes]
rs154144	0.85[ASN][1000 genomes]
rs159608	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs159610	0.85[ASN][1000 genomes]
rs159622	0.85[ASN][1000 genomes]
rs159624	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs159626	0.85[ASN][1000 genomes]
rs16890200	0.92[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs16890226	0.92[CHB][hapmap]
rs16890228	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs16890269	0.92[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16890276	0.92[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16890316	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs173945	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs17799450	0.96[GIH][hapmap]
rs181924	0.85[ASN][1000 genomes]
rs256348	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs256350	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs256353	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs34032696	0.84[EUR][1000 genomes]
rs6859121	0.91[CEU][hapmap];0.92[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868846	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6889984	0.82[JPT][hapmap];0.83[ASN][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	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10514880	RAB3C	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59106200-59115000	Weak transcription	HSMMtube	muscle
2	chr5:59109600-59113400	Weak transcription	Fetal Brain Male	brain
3	chr5:59110400-59115000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:59110400-59139000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:59111000-59114800	Weak transcription	HSMM	muscle
6	chr5:59111400-59122200	Weak transcription	Primary B cells from cord blood	blood
7	chr5:59112400-59114400	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr5:59112800-59113000	Enhancers	Brain Anterior Caudate	brain

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