Variant report

Variant	rs394009
Chromosome Location	chr17:19782553-19782554
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	chr17:19766743..19768696-chr17:19780331..19782628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs115326	0.88[ASN][1000 genomes]
rs118943	0.88[ASN][1000 genomes]
rs123081	0.92[ASN][1000 genomes]
rs150122	0.91[ASN][1000 genomes]
rs157388	0.90[ASN][1000 genomes]
rs157389	0.90[ASN][1000 genomes]
rs157390	0.90[ASN][1000 genomes]
rs157394	0.90[ASN][1000 genomes]
rs157395	0.92[ASN][1000 genomes]
rs157396	0.92[ASN][1000 genomes]
rs157399	0.92[ASN][1000 genomes]
rs157400	0.92[ASN][1000 genomes]
rs157401	0.92[ASN][1000 genomes]
rs157402	0.92[ASN][1000 genomes]
rs157408	0.92[ASN][1000 genomes]
rs157409	0.92[ASN][1000 genomes]
rs166839	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs169460	0.92[ASN][1000 genomes]
rs169512	0.88[ASN][1000 genomes]
rs172186	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs176098	0.88[ASN][1000 genomes]
rs182214	0.97[ASN][1000 genomes]
rs184006	0.88[ASN][1000 genomes]
rs188138	0.94[ASN][1000 genomes]
rs205087	0.82[ASN][1000 genomes]
rs205088	0.88[ASN][1000 genomes]
rs205092	0.85[ASN][1000 genomes]
rs205093	0.88[ASN][1000 genomes]
rs205094	0.88[ASN][1000 genomes]
rs205096	0.88[ASN][1000 genomes]
rs205098	0.87[ASN][1000 genomes]
rs205099	0.88[ASN][1000 genomes]
rs205100	0.88[ASN][1000 genomes]
rs205103	0.92[ASN][1000 genomes]
rs205104	0.92[ASN][1000 genomes]
rs205105	0.90[ASN][1000 genomes]
rs205107	0.88[ASN][1000 genomes]
rs205110	0.88[ASN][1000 genomes]
rs281325	0.94[ASN][1000 genomes]
rs281326	0.94[ASN][1000 genomes]
rs281327	0.94[ASN][1000 genomes]
rs281332	0.93[ASN][1000 genomes]
rs281333	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs281336	0.98[ASN][1000 genomes]
rs281337	0.97[ASN][1000 genomes]
rs281338	0.97[ASN][1000 genomes]
rs281339	0.95[ASN][1000 genomes]
rs281340	0.97[ASN][1000 genomes]
rs281341	0.96[ASN][1000 genomes]
rs281342	0.97[ASN][1000 genomes]
rs281343	0.97[ASN][1000 genomes]
rs281346	0.94[ASN][1000 genomes]
rs281348	0.94[ASN][1000 genomes]
rs281350	0.94[ASN][1000 genomes]
rs281351	0.94[ASN][1000 genomes]
rs281352	0.94[ASN][1000 genomes]
rs281354	0.94[ASN][1000 genomes]
rs281355	0.94[ASN][1000 genomes]
rs3098905	0.92[ASN][1000 genomes]
rs3098907	0.93[ASN][1000 genomes]
rs3101811	0.97[ASN][1000 genomes]
rs3101812	0.97[ASN][1000 genomes]
rs3101813	0.93[ASN][1000 genomes]
rs3101815	0.92[ASN][1000 genomes]
rs379703	0.90[ASN][1000 genomes]
rs383951	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs394008	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs421561	0.92[ASN][1000 genomes]
rs4586510	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1057469	chr17:19696714-19787062	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv2763158	chr17:19777544-19789227	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 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	chr17:19771600-19787000	Weak transcription	Gastric	stomach
2	chr17:19778600-19783200	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr17:19778800-19783400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr17:19780400-19783200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr17:19780400-19783200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:19780600-19783200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr17:19780600-19784200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr17:19780800-19784200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr17:19781000-19782800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr17:19781000-19784000	Enhancers	Primary T cells from cord blood	blood
11	chr17:19781200-19783000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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