Variant report

Variant	rs1102563
Chromosome Location	chr6:27160095-27160096
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	chr6:27154198..27156038-chr6:27159087..27161685,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10946904	0.94[YRI][hapmap]
rs1102558	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1102560	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1102564	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1102565	0.97[ASN][1000 genomes]
rs1156086	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13194053	0.81[YRI][hapmap]
rs13219181	0.81[YRI][hapmap]
rs2295603	0.84[CHD][hapmap]
rs2393915	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs28594674	0.82[AFR][1000 genomes]
rs3800309	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3823427	0.93[YRI][hapmap]
rs4236043	0.86[CEU][hapmap];0.93[AFR][1000 genomes]
rs4546474	0.84[CHD][hapmap]
rs4713069	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4713074	0.92[ASW][hapmap];0.86[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs5030956	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6456768	0.81[CHB][hapmap]
rs6902268	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6904071	0.81[YRI][hapmap]
rs6913660	0.81[YRI][hapmap]
rs6916555	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6917311	0.94[AFR][1000 genomes]
rs6940384	0.90[AFR][1000 genomes]
rs7759741	0.86[YRI][hapmap]
rs858967	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858968	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858969	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858970	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858972	1.00[JPT][hapmap]
rs858973	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs858974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs858976	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858977	0.94[ASN][1000 genomes]
rs858980	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs858982	0.85[EUR][1000 genomes]
rs926300	0.81[YRI][hapmap]
rs9379968	0.84[CHD][hapmap]
rs9468009	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9468010	0.86[AFR][1000 genomes]
rs9468013	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9468015	0.92[ASW][hapmap];0.86[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs994691	0.81[CHB][hapmap]
rs996247	0.93[AFR][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	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	esv3356749	chr6:27155446-27163661	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3350617	chr6:27158209-27160114	Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1102563	PGBD1	cis	parietal	SCAN
rs1102563	HMGN4	cis	Esophagus Mucosa	GTEx
rs1102563	ZNF391	cis	cerebellum	SCAN
rs1102563	ZNF184	cis	parietal	SCAN
rs1102563	HIST1H2AL	cis	cerebellum	SCAN
rs1102563	BTN3A2	cis	cerebellum	SCAN
rs1102563	ZSCAN23	cis	cerebellum	SCAN
rs1102563	ZNF323	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27156800-27161200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27156800-27162800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:27156800-27173000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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