Variant report

Variant	rs1883403
Chromosome Location	chr6:27350329-27350330
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	chr6:27338163..27340340-chr6:27350329..27352907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204789	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1011665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946915	0.93[ASN][1000 genomes]
rs12526495	0.86[ASN][1000 genomes]
rs12529458	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs12663650	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12664996	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13220817	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064093	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2206250	0.83[CHD][hapmap]
rs2235232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2393926	0.94[ASN][1000 genomes]
rs2393962	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs2393964	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs4711152	0.90[ASN][1000 genomes]
rs4713098	0.82[ASN][1000 genomes]
rs4713099	0.82[ASN][1000 genomes]
rs6901629	0.84[AFR][1000 genomes]
rs6913166	0.83[ASW][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914864	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6922815	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71559025	0.85[ASN][1000 genomes]
rs764284	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7761966	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs7772739	0.94[ASN][1000 genomes]
rs9357038	0.97[ASN][1000 genomes]
rs9379980	0.82[ASN][1000 genomes]
rs9393813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1883403	ZSCAN23	cis	cerebellum	SCAN
rs1883403	HIST1H3B	cis	cerebellum	SCAN
rs1883403	ZNF391	cis	Thyroid	GTEx
rs1883403	ZNF391	cis	cerebellum	SCAN
rs1883403	ZNF391	cis	Artery Tibial	GTEx
rs1883403	ZNF391	cis	lung	GTEx
rs1883403	ZNF204P	cis	parietal	SCAN
rs1883403	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs1883403	ZNF204P	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27343200-27356200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:27346800-27356200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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