Variant report

Variant	rs17651538
Chromosome Location	chr5:75552501-75552502
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75030757..75031393-chr5:75551873..75552728,2	K562	blood:
2	chr5:75370186..75371274-chr5:75551816..75552790,4	MCF-7	breast:
3	chr5:75534573..75536259-chr5:75552032..75554842,2	K562	blood:
4	chr5:75030734..75031635-chr5:75551827..75552781,3	MCF-7	breast:
5	chr5:75030589..75031686-chr5:75551613..75552708,6	MCF-7	breast:
6	chr5:75470625..75471456-chr5:75551799..75552684,5	MCF-7	breast:
7	chr5:75311875..75312445-chr5:75551956..75552709,2	MCF-7	breast:
8	chr5:75370056..75370744-chr5:75551849..75552754,4	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10473981	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2937721	0.84[AMR][1000 genomes]
rs2972825	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2972827	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4266386	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4481336	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4703704	0.82[AMR][1000 genomes]
rs4704302	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6863252	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs6865629	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6884646	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6891813	0.86[EUR][1000 genomes]
rs6891999	0.85[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs6894289	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7722717	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7735980	0.89[AMR][1000 genomes];0.86[EUR][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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17651538	ZBED3	cis	cerebellum	SCAN
rs17651538	AGGF1	cis	cerebellum	SCAN
rs17651538	DMGDH	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75550200-75553200	Weak transcription	Gastric	stomach
2	chr5:75551800-75552600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:75551800-75552600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:75551800-75552600	Enhancers	Fetal Heart	heart
5	chr5:75551800-75552800	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr5:75551800-75555000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr5:75551800-75555200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:75552000-75552600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:75552000-75552600	Enhancers	Primary hematopoietic stem cells	blood
10	chr5:75552000-75552600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr5:75552000-75553000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:75552000-75553400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:75552200-75553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links