Variant report

Variant	rs4957554
Chromosome Location	chr5:107745376-107745377
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	chr5:107715395..107721337-chr5:107744476..107755519,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10036343	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10041907	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10074085	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10075907	0.81[CHB][hapmap]
rs10455007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743651	0.81[CHB][hapmap]
rs2029104	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2044710	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2112306	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2122158	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2416188	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2922423	0.81[CHB][hapmap]
rs2922424	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2922426	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2922428	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2966795	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2966799	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4541643	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4957553	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4957753	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7708996	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7717747	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7726298	0.80[CHB][hapmap]
rs9326725	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs989001	0.81[CHB][hapmap];0.81[JPT][hapmap]

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	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	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv968111	chr5:107743066-107755991	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4957554	NCRNA00219	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107735000-107745800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:107745200-107745400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:107745200-107745400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:107745200-107745600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:107745200-107746000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:107745200-107746800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:107745200-107747600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:107745200-107747800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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