Variant report

Variant	rs4407661
Chromosome Location	chr5:1974282-1974283
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	chr5:1964453..1969869-chr5:1973026..1976293,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248597	Chromatin interaction
ENSG00000249731	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10035144	0.98[ASN][1000 genomes]
rs10043083	0.91[ASN][1000 genomes]
rs10045683	0.97[ASN][1000 genomes]
rs10053882	0.80[ASN][1000 genomes]
rs1017924	1.00[ASN][1000 genomes]
rs10474733	0.84[ASN][1000 genomes]
rs10474734	0.84[ASN][1000 genomes]
rs11133918	1.00[ASN][1000 genomes]
rs1123381	1.00[ASN][1000 genomes]
rs1123390	0.99[ASN][1000 genomes]
rs1123391	0.99[ASN][1000 genomes]
rs11749073	0.84[ASN][1000 genomes]
rs11952205	0.94[ASN][1000 genomes]
rs12188545	0.96[ASN][1000 genomes]
rs12654102	0.83[ASN][1000 genomes]
rs12716127	0.98[ASN][1000 genomes]
rs13166888	0.97[ASN][1000 genomes]
rs13170991	0.80[ASN][1000 genomes]
rs1486937	0.91[ASN][1000 genomes]
rs1601641	0.91[ASN][1000 genomes]
rs3902820	0.91[ASN][1000 genomes]
rs4246751	0.80[ASN][1000 genomes]
rs4246752	1.00[ASN][1000 genomes]
rs4371796	0.97[ASN][1000 genomes]
rs4382203	0.80[ASN][1000 genomes]
rs4526149	0.91[ASN][1000 genomes]
rs4975777	1.00[ASN][1000 genomes]
rs4975779	0.92[ASN][1000 genomes]
rs4975786	0.84[ASN][1000 genomes]
rs55860207	0.88[ASN][1000 genomes]
rs57434783	0.98[ASN][1000 genomes]
rs61656301	0.90[ASN][1000 genomes]
rs62337135	0.93[ASN][1000 genomes]
rs67659713	0.99[ASN][1000 genomes]
rs7445193	0.80[ASN][1000 genomes]
rs872807	0.80[ASN][1000 genomes]
rs901504	0.80[ASN][1000 genomes]
rs9312970	0.84[ASN][1000 genomes]
rs965276	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1973400-1974400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr5:1973400-1974400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr5:1973400-1975800	Flanking Active TSS	HMEC	breast
4	chr5:1973600-1975600	Flanking Active TSS	NHEK	skin
5	chr5:1973800-1974400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:1973800-1974400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:1973800-1974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:1973800-1974800	Weak transcription	Esophagus	oesophagus
9	chr5:1974000-1974400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr5:1974000-1974400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr5:1974000-1975600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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