Variant report

Variant	rs16998327
Chromosome Location	chr20:52312830-52312831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69260613..69262497-chr20:52311916..52313959,2	MCF-7	breast:
2	chr17:59660286..59662351-chr20:52311555..52314413,2	MCF-7	breast:
3	chr17:56735041..56736907-chr20:52311240..52314004,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSHZ2-10	chr20:52311844-52313139	NONHSAT080400

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs58014966	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60003803	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60192794	0.93[AFR][1000 genomes]
rs6022667	0.92[EUR][1000 genomes]
rs6022672	0.81[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs6022675	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6022677	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6022679	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61141992	0.92[AFR][1000 genomes]
rs66951711	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7264081	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73134247	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73283718	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7348874	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7348908	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
4	nsv912935	chr20:52221906-52337118	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	101 gene(s)	inside rSNPs	diseases
5	nsv912936	chr20:52250876-52344962	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv912937	chr20:52251863-52344962	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
7	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
8	nsv518277	chr20:52276452-52315311	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
9	nsv912938	chr20:52276452-52328338	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv437185	chr20:52300359-52330053	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv517748	chr20:52304108-52315311	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv437186	chr20:52309454-52315311	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52309400-52316000	Weak transcription	HepG2	liver
2	chr20:52309400-52324800	Weak transcription	Spleen	Spleen
3	chr20:52309600-52316000	Weak transcription	Adipose Nuclei	Adipose
4	chr20:52310000-52314600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:52310200-52313400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr20:52310200-52314600	Weak transcription	GM12878-XiMat	blood
7	chr20:52310200-52314800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr20:52310200-52316200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr20:52310200-52322000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr20:52310400-52313000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr20:52310400-52314800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:52310400-52316000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr20:52310400-52316400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr20:52310400-52317200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr20:52310400-52317400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr20:52310400-52317400	Weak transcription	Fetal Thymus	thymus
17	chr20:52310600-52316200	Weak transcription	Dnd41	blood
18	chr20:52311200-52317400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:52311400-52317600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr20:52312400-52313800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr20:52312800-52313000	Enhancers	H9 Cell Line	embryonic stem cell

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