Variant report

Variant	rs6124418
Chromosome Location	chr20:40759450-40759451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40758696..40760777-chr20:40762885..40764825,2	MCF-7	breast:
2	chr20:40753966..40756056-chr20:40757861..40760151,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12625660	0.87[EUR][1000 genomes]
rs12625736	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12625871	0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs1569552	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs16986553	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17221018	0.86[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17221137	0.86[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17312515	0.86[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2223422	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4281967	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs59458271	0.83[AFR][1000 genomes]
rs59996685	0.83[AFR][1000 genomes]
rs6029997	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6093610	1.00[CEU][hapmap]
rs6124419	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6124420	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs6124431	0.87[EUR][1000 genomes]
rs6130039	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs6130040	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6130042	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6130043	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6130051	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs6130052	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs6130055	0.96[EUR][1000 genomes]
rs8183826	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40747800-40762400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:40757600-40765800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:40758800-40760800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:40759400-40766400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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