Variant report

Variant	rs10828225
Chromosome Location	chr10:21543040-21543041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:21536651..21539154-chr10:21541476..21543888,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232853	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10400156	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828226	1.00[ASN][1000 genomes]
rs11012606	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11012613	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12262659	1.00[CHB][hapmap]
rs12762123	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12762293	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12770644	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1482899	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359929	1.00[ASN][1000 genomes]
rs35199186	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3847375	1.00[CHB][hapmap]
rs60959763	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6482170	0.83[ASN][1000 genomes]
rs67484996	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7069644	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs7076532	1.00[ASN][1000 genomes]
rs7085330	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7090954	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092555	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71486488	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7894121	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7896926	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7905100	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7905278	1.00[ASN][1000 genomes]
rs7910610	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921613	0.81[AMR][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	nsv530148	chr10:21065080-21724565	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv971871	chr10:21460392-21579987	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831807	chr10:21509185-21688043	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10828225	NEBL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:21522000-21549600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr10:21522200-21549200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr10:21524000-21548000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:21524000-21549000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:21524000-21549400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:21530600-21549600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr10:21539600-21549400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:21542800-21548200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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