Variant report

Variant	rs4140521
Chromosome Location	chr20:40869234-40869235
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40857397..40860035-chr20:40866668..40870281,3	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1014757	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs11907691	0.92[ASN][1000 genomes]
rs12625238	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13040788	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs16986670	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1883376	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1883377	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs1883378	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1984399	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2143008	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2143632	0.90[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2179336	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2206168	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2206169	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2223425	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2223426	0.81[ASN][1000 genomes]
rs2223718	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2867061	0.92[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2867062	0.92[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2867063	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2903465	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4331574	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4425144	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4507153	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs6016705	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6016707	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6016708	0.80[ASN][1000 genomes]
rs6016709	0.80[ASN][1000 genomes]
rs6016710	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6016711	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6016712	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6016713	0.81[ASN][1000 genomes]
rs6016716	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6016726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6016732	0.82[TSI][hapmap]
rs6030023	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs6030026	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6030027	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6030029	0.81[ASN][1000 genomes]
rs6030033	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6030035	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6030036	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs6030037	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6030056	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6030058	0.81[CHB][hapmap]
rs6030061	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6030069	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6030070	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6030071	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs6030073	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6030076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6030078	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6030081	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6030082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6030083	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6030084	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs6030085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6030087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6030088	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6030089	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs6030096	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6030100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6030101	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6065450	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6065451	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6072651	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6072672	0.92[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6093584	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6093588	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6093589	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6093598	0.81[JPT][hapmap]
rs6102713	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6124427	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6124429	0.82[ASN][1000 genomes]
rs6124435	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6130068	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs6130071	0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs6130073	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs6130074	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs6130076	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6130081	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6130091	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7270492	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs727336	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs727337	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs728373	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs728374	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs742290	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs742291	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs926647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs932358	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs979634	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[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	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4140521	RBPJL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40861800-40874600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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