Variant report

Variant	rs11948261
Chromosome Location	chr5:107753691-107753692
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	chr5:107714638..107722268-chr5:107749146..107755039,15	MCF-7	breast:
2	chr5:107715395..107721337-chr5:107744476..107755519,20	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FER-2	chr5:107753413-107753700	XLOC_004500
2	lnc-FER-2	chr5:107753413-107753700	NONHSAT103121
3	lnc-FER-2	chr5:107753412-107753700	NONHSAT103122

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10035966	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10045508	0.92[EUR][1000 genomes]
rs10054662	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061049	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078397	0.92[EUR][1000 genomes]
rs10463587	0.93[EUR][1000 genomes]
rs11240962	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11742268	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11949077	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11949079	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12187433	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361152	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1510967	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17388874	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454114	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112303	0.96[ASN][1000 genomes]
rs28572757	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28752150	1.00[ASN][1000 genomes]
rs4413518	0.90[EUR][1000 genomes]
rs57370105	0.92[ASN][1000 genomes]
rs59423465	0.89[EUR][1000 genomes]
rs60045633	0.90[EUR][1000 genomes]
rs60896544	0.89[EUR][1000 genomes]
rs62362279	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62362281	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62362302	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876738	0.87[EUR][1000 genomes]
rs6881232	0.89[EUR][1000 genomes]
rs6895295	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7714342	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720469	0.93[EUR][1000 genomes]
rs7720841	0.90[EUR][1000 genomes]
rs9326727	0.87[AMR][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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv968111	chr5:107743066-107755991	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107752800-107753800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:107753600-107754000	Enhancers	Psoas Muscle	Psoas
3	chr5:107753600-107754000	Enhancers	Skeletal Muscle Male	skeletal muscle

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