Variant report

Variant	rs9672298
Chromosome Location	chr15:41912368-41912369
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41900433..41903180-chr15:41911539..41913856,2	K562	blood:
2	chr15:41911067..41913246-chr15:41921472..41923758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260926	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1105881	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs11070343	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107858	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11629678	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634956	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs11639043	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440747	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs16952372	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs16971976	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17676742	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17677199	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17677991	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17678138	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17678552	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17678767	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs17733613	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17734856	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs1918310	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs2303518	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28526689	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28708888	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4923905	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924564	0.93[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4924570	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4924575	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs8023311	0.93[ASN][1000 genomes]
rs8035855	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs9672360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672671	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9672298	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs9672298	MGA	cis	lesional skin	skin_eQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41909000-41913000	Weak transcription	Placenta	Placenta
2	chr15:41909600-41912800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:41910200-41912800	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:41912200-41912600	Enhancers	Hela-S3	cervix

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