Variant report

Variant	rs4663990
Chromosome Location	chr2:234862040-234862041
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	chr2:234861030..234863586-chr2:234874860..234877579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144481	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1003540	1.00[YRI][hapmap]
rs10166942	1.00[YRI][hapmap]
rs10170399	1.00[YRI][hapmap]
rs10189040	0.83[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs10490014	0.87[CEU][hapmap];0.81[AFR][1000 genomes]
rs10929319	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11563060	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11563063	0.89[YRI][hapmap]
rs11563216	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892538	0.89[YRI][hapmap]
rs1965629	1.00[YRI][hapmap]
rs2108809	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2215173	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2362290	1.00[YRI][hapmap]
rs2362292	0.82[AMR][1000 genomes]
rs28946911	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs28953468	0.87[CEU][hapmap];0.83[AFR][1000 genomes]
rs4233636	1.00[YRI][hapmap]
rs4663986	1.00[YRI][hapmap]
rs4663988	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6431648	1.00[YRI][hapmap]
rs6709005	1.00[YRI][hapmap]
rs6711120	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs6712540	0.84[AMR][1000 genomes]
rs6712893	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6738375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6738979	1.00[YRI][hapmap]
rs6740118	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737636	1.00[YRI][hapmap]
rs758275	0.83[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs758276	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs758277	0.88[YRI][hapmap]
rs7597012	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604471	1.00[YRI][hapmap]
rs887065	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs917435	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr2:234849400-234883400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:234849600-234873800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234861600-234862600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:234861800-234863000	Enhancers	Cortex derived primary cultured neurospheres	brain

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