Variant report

Variant	rs9397398
Chromosome Location	chr6:150193603-150193604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150182195..150187725-chr6:150188544..150196234,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1334510	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889471	0.82[EUR][1000 genomes]
rs2095376	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342767	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2342768	0.82[EUR][1000 genomes]
rs2342769	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2342770	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3823021	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4458704	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4869763	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4869764	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4870116	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6557133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933882	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6935829	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6939761	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7740145	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742692	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742993	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7744821	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7747435	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7747457	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7753544	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7756850	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757972	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757984	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7758020	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7758033	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763719	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7763849	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764376	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767588	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7767592	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7768626	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768665	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7769118	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771014	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7774787	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9322225	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322228	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371215	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371223	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9371504	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9371505	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9371533	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9371541	0.82[ASN][1000 genomes]
rs9371542	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9371544	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9383577	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383584	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383912	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383914	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383921	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383940	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397058	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9397420	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9397434	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9478192	0.84[EUR][1000 genomes]
rs9968871	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9969044	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9397398	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9397398	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9397398	NUP43	cis	Whole Blood	GTEx
rs9397398	RP11-350J20.5	cis	lung	GTEx
rs9397398	RAET1G	cis	Thyroid	GTEx
rs9397398	RAET1G	cis	Artery Tibial	GTEx
rs9397398	RP11-350J20.9	cis	lung	GTEx
rs9397398	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9397398	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9397398	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9397398	RP11-350J20.9	cis	Heart Left Ventricle	GTEx
rs9397398	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9397398	RP11-350J20.5	cis	Thyroid	GTEx
rs9397398	RP11-350J20.5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150186200-150194400	Weak transcription	Pancreas	Pancrea

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