Variant report

Variant	rs10490092
Chromosome Location	chr2:58892049-58892050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58888823..58892438-chr2:58904380..58907466,3	K562	blood:
2	chr2:58888614..58890571-chr2:58890979..58892599,2	MCF-7	breast:
3	chr2:58890237..58893053-chr2:58893289..58896323,3	K562	blood:
4	chr2:58890762..58894483-chr2:58899743..58902902,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10490093	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13026438	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421824	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17049642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17190597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17190618	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17269154	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17269182	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549476	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17549656	0.94[EUR][1000 genomes]
rs17549677	0.97[EUR][1000 genomes]
rs17549712	0.98[EUR][1000 genomes]
rs17549754	0.96[EUR][1000 genomes]
rs17549803	0.96[EUR][1000 genomes]
rs17614872	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17614895	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17615036	0.92[EUR][1000 genomes]
rs17615120	0.97[EUR][1000 genomes]
rs17615185	0.96[EUR][1000 genomes]
rs17615279	0.96[EUR][1000 genomes]
rs17615309	0.96[EUR][1000 genomes]
rs17615381	0.96[EUR][1000 genomes]
rs1922781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950160	0.98[EUR][1000 genomes]
rs2204913	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55645922	0.98[EUR][1000 genomes]
rs55745617	0.98[EUR][1000 genomes]
rs56174720	0.97[EUR][1000 genomes]
rs56266136	0.98[EUR][1000 genomes]
rs56365214	0.97[EUR][1000 genomes]
rs60018257	0.96[EUR][1000 genomes]
rs7419776	0.87[ASN][1000 genomes]
rs984881	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984883	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1012213	chr2:58671881-58893730	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv535736	chr2:58671881-58893730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv431180	chr2:58857542-59178687	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10490092	LOC339803	cis	parietal	SCAN
rs10490092	SPTBN1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58884600-58892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:58884600-58893400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:58891400-58892600	Enhancers	Brain Germinal Matrix	brain
4	chr2:58891600-58892200	Enhancers	Fetal Brain Female	brain
5	chr2:58891600-58893800	Enhancers	K562	blood
6	chr2:58891800-58892200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:58891800-58892400	Enhancers	HUVEC	blood vessel

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