Variant report

Variant	rs2823154
Chromosome Location	chr21:16587487-16587488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16249191..16252092-chr21:16587437..16590052,2	MCF-7	breast:
2	chr21:16584909..16587844-chr21:16591132..16593725,3	K562	blood:
3	chr21:16584216..16586791-chr21:16587079..16588631,2	MCF-7	breast:
4	chr21:16586904..16589804-chr21:16590773..16592275,2	K562	blood:
5	chr21:16421751..16443998-chr21:16557859..16589610,273	MCF-7	breast:
6	chr21:16586940..16589372-chr21:16591214..16594501,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction
ENSG00000236471	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11909130	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483396	0.86[EUR][1000 genomes]
rs12483484	0.88[EUR][1000 genomes]
rs13046557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13046821	0.89[EUR][1000 genomes]
rs13051325	0.89[EUR][1000 genomes]
rs13052858	0.88[EUR][1000 genomes]
rs2064040	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2823148	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823151	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823165	0.82[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2823168	0.82[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2823169	0.82[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2823172	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2823173	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2823174	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2823175	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2823176	0.89[EUR][1000 genomes]
rs2823178	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2823179	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2823180	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2823181	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs6517301	0.82[EUR][1000 genomes]
rs6517302	0.83[EUR][1000 genomes]
rs6517303	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs7281303	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs8131982	0.88[EUR][1000 genomes]
rs9808777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3454967	chr21:16586481-16591979	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1839906	chr21:16587118-16589135	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv587051	chr21:16587477-16589135	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823154	SAMSN1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16585400-16587800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr21:16585400-16592000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr21:16585600-16591400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr21:16586000-16591400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr21:16586400-16592400	Weak transcription	Liver	Liver
6	chr21:16586600-16587800	Weak transcription	HepG2	liver

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