Variant report

Variant	rs6127090
Chromosome Location	chr20:52694254-52694255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52691602..52694513-chr20:52873450..52876265,2	MCF-7	breast:
2	chr20:46414990..46416847-chr20:52691422..52694318,2	MCF-7	breast:
3	chr17:56707910..56710399-chr20:52692495..52695417,3	MCF-7	breast:
4	chr17:56707573..56710452-chr20:52690315..52697249,11	MCF-7	breast:
5	chr20:52692734..52695729-chr20:55845118..55846934,2	MCF-7	breast:
6	chr17:56735126..56737040-chr20:52692094..52694559,3	MCF-7	breast:
7	chr20:52209032..52211592-chr20:52693002..52694936,2	MCF-7	breast:
8	chr20:46413800..46415438-chr20:52692671..52695400,2	MCF-7	breast:
9	chr17:57918096..57920915-chr20:52692423..52694442,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171940	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000196562	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12624475	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12624494	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12624748	1.00[YRI][hapmap]
rs12624750	1.00[YRI][hapmap]
rs12625278	1.00[YRI][hapmap]
rs12625283	1.00[YRI][hapmap]
rs12625949	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998867	1.00[YRI][hapmap]
rs16998871	1.00[YRI][hapmap]
rs16998873	1.00[YRI][hapmap]
rs2020975	1.00[YRI][hapmap]
rs2107328	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2870305	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2870306	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs290400	0.93[ASN][1000 genomes]
rs34522098	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3787540	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3787544	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3787545	1.00[YRI][hapmap]
rs3787551	1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs412429	1.00[CEU][hapmap]
rs41304655	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41308729	0.95[ASN][1000 genomes]
rs58634156	0.87[AMR][1000 genomes]
rs6123346	1.00[YRI][hapmap]
rs6123348	1.00[YRI][hapmap]
rs6123349	1.00[YRI][hapmap]
rs6123350	1.00[YRI][hapmap]
rs6123351	1.00[YRI][hapmap]
rs6123352	0.86[JPT][hapmap]
rs6123353	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6123354	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6123355	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6123356	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127075	1.00[YRI][hapmap]
rs6127076	1.00[YRI][hapmap]
rs6127080	1.00[YRI][hapmap]
rs6127081	1.00[YRI][hapmap]
rs6127083	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6127084	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs6127085	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6127086	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127088	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73134888	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs899049	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52691200-52694800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr20:52693000-52694800	Weak transcription	GM12878-XiMat	blood
3	chr20:52693000-52701200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr20:52693400-52698600	Weak transcription	Stomach Mucosa	stomach
5	chr20:52693600-52694600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr20:52693800-52697400	Enhancers	Primary hematopoietic stem cells	blood
7	chr20:52693800-52699200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr20:52694200-52694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:52694200-52694800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr20:52694200-52696200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr20:52694200-52696400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr20:52694200-52697600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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