Variant report

Variant	rs10490249
Chromosome Location	chr2:58519530-58519531
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58513497..58515755-chr2:58518293..58520295,2	MCF-7	breast:
2	chr2:58516462..58520346-chr2:58521075..58523718,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10168877	0.82[EUR][1000 genomes]
rs10178765	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10490250	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11125748	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1156588	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11891166	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11891414	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12151813	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713381	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13399274	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412643	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215960	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2861377	0.85[EUR][1000 genomes]
rs34286598	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34520788	0.82[EUR][1000 genomes]
rs34574366	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34692015	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35459416	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4464258	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60851549	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71418489	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725451	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs725452	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594908	0.81[ASN][1000 genomes]
rs7595474	0.87[EUR][1000 genomes]
rs9646985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58514800-58519800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:58519400-58520000	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:58519400-58520800	Enhancers	Brain Hippocampus Middle	brain
4	chr2:58519400-58521200	Enhancers	Brain Substantia Nigra	brain
5	chr2:58519400-58521600	Enhancers	Brain Angular Gyrus	brain

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