Variant report

Variant	rs9474643
Chromosome Location	chr6:53613433-53613434
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	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11759427	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11759473	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12662433	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663216	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs3003492	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs3003498	0.82[CHB][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs3813850	1.00[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs4478409	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486000	0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4712042	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4715421	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57853292	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62399939	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458956	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6905563	0.81[JPT][hapmap]
rs7759593	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9463970	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9463971	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463975	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463976	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9463996	0.83[JPT][hapmap]
rs9474647	1.00[CEU][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474650	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9474651	0.81[AMR][1000 genomes];0.96[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9474643	LRRC1	cis	multi-tissue	Pritchard
rs9474643	C6orf142	cis	cerebellum	SCAN
rs9474643	RAB23	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
4	chr6:53610200-53614000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:53612000-53614800	Weak transcription	Hela-S3	cervix
6	chr6:53612200-53614800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53612200-53614800	Weak transcription	NHEK	skin
8	chr6:53612200-53616200	Weak transcription	HMEC	breast
9	chr6:53612200-53616600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:53612200-53616800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:53612200-53617400	Weak transcription	Placenta	Placenta

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