Variant report

Variant	rs16999504
Chromosome Location	chr20:52958282-52958283
allele	A/C
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	chr20:52892973..52894968-chr20:52956980..52958556,2	MCF-7	breast:
2	chr20:52947709..52951079-chr20:52955408..52958637,4	MCF-7	breast:
3	chr20:52861825..52864272-chr20:52956863..52959337,2	MCF-7	breast:
4	chr20:52955311..52960636-chr20:52963948..52966775,4	MCF-7	breast:
5	chr12:50536506..50537503-chr20:52957817..52958407,2	MCF-7	breast:
6	chr20:52823411..52827857-chr20:52956007..52962022,9	MCF-7	breast:
7	chr20:52956264..52958704-chr20:53136561..53138207,2	MCF-7	breast:
8	chr20:52957064..52959136-chr20:53012315..53013962,2	MCF-7	breast:
9	chr12:753066..755991-chr20:52956460..52959168,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1382013	0.91[EUR][1000 genomes]
rs16999452	0.91[EUR][1000 genomes]
rs16999466	0.91[EUR][1000 genomes]
rs16999487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999513	0.91[EUR][1000 genomes]
rs2219733	0.91[EUR][1000 genomes]
rs28373824	0.91[EUR][1000 genomes]
rs28516647	0.91[EUR][1000 genomes]
rs2870321	0.91[EUR][1000 genomes]
rs4289245	0.91[EUR][1000 genomes]
rs4493332	0.91[EUR][1000 genomes]
rs4541294	0.91[EUR][1000 genomes]
rs4599177	0.91[EUR][1000 genomes]
rs4619676	0.91[EUR][1000 genomes]
rs56149353	0.91[EUR][1000 genomes]
rs56268746	0.91[EUR][1000 genomes]
rs58025571	0.91[EUR][1000 genomes]
rs58475917	0.91[EUR][1000 genomes]
rs58894404	0.91[EUR][1000 genomes]
rs59811202	0.91[EUR][1000 genomes]
rs6013973	0.83[EUR][1000 genomes]
rs6013974	0.83[EUR][1000 genomes]
rs6013977	0.91[EUR][1000 genomes]
rs6013980	1.00[EUR][1000 genomes]
rs6013981	1.00[EUR][1000 genomes]
rs6023065	0.83[EUR][1000 genomes]
rs6023109	0.91[EUR][1000 genomes]
rs6023111	0.91[EUR][1000 genomes]
rs6023113	0.91[EUR][1000 genomes]
rs6023114	0.91[EUR][1000 genomes]
rs6023116	0.91[EUR][1000 genomes]
rs6023118	0.91[EUR][1000 genomes]
rs6023119	0.91[EUR][1000 genomes]
rs6023120	0.91[EUR][1000 genomes]
rs6023124	0.91[EUR][1000 genomes]
rs6023126	0.91[EUR][1000 genomes]
rs6023128	0.83[EUR][1000 genomes]
rs6023139	0.91[EUR][1000 genomes]
rs6023144	1.00[EUR][1000 genomes]
rs6097927	0.91[EUR][1000 genomes]
rs723128	0.91[EUR][1000 genomes]
rs7265137	0.91[EUR][1000 genomes]
rs7265354	0.91[EUR][1000 genomes]
rs73137415	0.83[EUR][1000 genomes]
rs73137442	0.83[EUR][1000 genomes]
rs73137444	0.83[EUR][1000 genomes]
rs73137446	0.83[EUR][1000 genomes]
rs73137451	0.83[EUR][1000 genomes]
rs73139406	0.83[EUR][1000 genomes]
rs73139426	0.83[EUR][1000 genomes]
rs73139427	0.91[EUR][1000 genomes]
rs73139465	0.91[EUR][1000 genomes]
rs73139467	0.91[EUR][1000 genomes]
rs73139469	0.91[EUR][1000 genomes]
rs73139472	0.91[EUR][1000 genomes]
rs73139477	0.91[EUR][1000 genomes]
rs7347628	0.91[EUR][1000 genomes]
rs8119798	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 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	chr20:52956000-52963800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52956600-52958400	Enhancers	Osteobl	bone
3	chr20:52956600-52958600	Enhancers	Hela-S3	cervix
4	chr20:52957200-52958400	Enhancers	NHDF-Ad	bronchial
5	chr20:52957400-52961400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr20:52957600-52958400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:52957600-52959200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:52957600-52959200	Weak transcription	Fetal Brain Female	brain
9	chr20:52957600-52962000	Weak transcription	Colon Smooth Muscle	Colon
10	chr20:52957800-52958600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:52957800-52958800	Weak transcription	Brain Germinal Matrix	brain
12	chr20:52957800-52960200	Weak transcription	A549	lung
13	chr20:52957800-52960800	Enhancers	HUVEC	blood vessel
14	chr20:52958000-52959800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:52958000-52961200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:52958000-52961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:52958000-52961400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr20:52958200-52961200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr20:52958200-52961200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr20:52958200-52961400	Weak transcription	Psoas Muscle	Psoas
21	chr20:52958200-52961400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links