Variant report

Variant	rs4485554
Chromosome Location	chr2:64546466-64546467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64542272..64545159-chr2:64546198..64548765,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10187442	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030407	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030409	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1030410	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673882	0.84[ASN][1000 genomes]
rs11682772	0.86[ASN][1000 genomes]
rs11683866	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs11883600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365474	0.81[ASN][1000 genomes]
rs1365475	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1426699	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1426701	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1426702	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1426712	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1974976	0.85[ASN][1000 genomes]
rs2059630	0.81[CHB][hapmap]
rs2263647	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278184	0.86[ASN][1000 genomes]
rs2555423	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2555448	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597511	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546064	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546065	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66506765	0.81[ASN][1000 genomes]
rs6714101	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724171	0.81[ASN][1000 genomes]
rs6737527	0.81[ASN][1000 genomes]
rs6740438	0.81[ASN][1000 genomes]
rs6748843	0.81[ASN][1000 genomes]
rs6758664	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561343	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7565077	0.83[ASN][1000 genomes]
rs7585084	0.84[ASN][1000 genomes]
rs7601758	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7601803	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890478	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919122	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs919123	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919124	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919125	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919126	0.93[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs919127	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs930020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64539800-64549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
3	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:64540800-64549600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
6	chr2:64542200-64547200	Weak transcription	Brain Germinal Matrix	brain
7	chr2:64543800-64549000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:64543800-64549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:64544000-64547800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:64544400-64548400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:64546000-64552000	Weak transcription	Thymus	Thymus
12	chr2:64546200-64549000	Weak transcription	Fetal Lung	lung

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