Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165253102..165255836-chr1:165256006..165257807,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11807536	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12068638	0.81[ASN][1000 genomes]
rs12097516	0.81[ASN][1000 genomes]
rs12404307	0.80[TSI][hapmap]
rs12752351	0.91[ASN][1000 genomes]
rs1807798	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.99[ASN][1000 genomes]
rs1833030	0.92[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2174696	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs4656442	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657424	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4657425	0.81[ASN][1000 genomes]
rs4657426	0.80[ASN][1000 genomes]
rs4657427	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4657428	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4657429	0.81[ASN][1000 genomes]
rs4657431	0.91[ASN][1000 genomes]
rs58462518	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59327172	0.81[ASN][1000 genomes]
rs6662349	0.82[CEU][hapmap]
rs7528111	0.83[ASW][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7528546	0.91[ASN][1000 genomes]
rs7530861	0.81[ASN][1000 genomes]
rs7534017	0.99[EUR][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	nsv869712	chr1:164866810-165299085	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7540476	CASQ1	cis	cerebellum	SCAN
rs7540476	LRRC52	cis	cerebellum	SCAN
rs7540476	B4GALT3	cis	parietal	SCAN
rs7540476	UCK2	cis	cerebellum	SCAN
rs7540476	SLAMF1	cis	cerebellum	SCAN
rs7540476	CYFIP2	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165248800-165256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165251600-165256600	Weak transcription	HepG2	liver
3	chr1:165253600-165258200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:165254600-165258800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:165254800-165257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:165254800-165258800	Enhancers	Liver	Liver
7	chr1:165255600-165258200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr1:165256000-165256400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:165256000-165258000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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