Variant report

Variant	rs3908469
Chromosome Location	chr1:216111962-216111963
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216109491..216112444-chr1:216113554..216115668,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10864214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120694	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11120697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs12034100	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12046356	0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12091359	1.00[YRI][hapmap]
rs12562080	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1347629	0.82[CHB][hapmap]
rs1836937	0.80[ASN][1000 genomes]
rs1934423	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365632	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3845529	0.82[CHB][hapmap]
rs4100655	0.82[CHB][hapmap]
rs4655288	1.00[YRI][hapmap]
rs4655433	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4655437	0.82[CHB][hapmap]
rs492474	0.93[CHB][hapmap]
rs498911	0.93[CHB][hapmap]
rs513746	0.93[CHB][hapmap]
rs517577	0.94[CHB][hapmap]
rs633846	0.88[CHB][hapmap]
rs646576	0.94[CHB][hapmap]
rs647908	0.94[CHB][hapmap]
rs662355	0.94[CHB][hapmap]
rs6661521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs6665202	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6675583	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs772713	0.93[CHB][hapmap]
rs942837	0.94[CHB][hapmap]
rs942838	1.00[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv428599	chr1:216086224-216267211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216111600-216112400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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