Variant report

Variant	rs13420500
Chromosome Location	chr2:190934874-190934875
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

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190662961..190664099-chr2:190934762..190935615,4	MCF-7	breast:
2	chr2:190525494..190527928-chr2:190932938..190936738,3	MCF-7	breast:
3	chr2:190615890..190616537-chr2:190934809..190935547,3	MCF-7	breast:
4	chr2:190888760..190889590-chr2:190934656..190935555,3	MCF-7	breast:
5	chr2:190598560..190600612-chr2:190933764..190936745,2	MCF-7	breast:
6	chr2:190525462..190526385-chr2:190934699..190935692,9	MCF-7	breast:
7	chr2:190615478..190616969-chr2:190934827..190935711,5	MCF-7	breast:
8	chr2:190929529..190932030-chr2:190933880..190936780,2	MCF-7	breast:
9	chr2:190525361..190526350-chr2:190934745..190935732,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10804031	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs13401889	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474359	0.91[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1967606	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791783	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4853626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57566211	0.80[EUR][1000 genomes]
rs7570532	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7571669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3439178	chr2:190877215-191124499	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13420500	PMS1	cis	parietal	SCAN
rs13420500	ASNSD1	cis	parietal	SCAN
rs13420500	ORMDL1	cis	cerebellum	SCAN
rs13420500	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs13420500	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs13420500	ASNSD1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190934600-190935000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:190934600-190935000	Enhancers	Adipose Nuclei	Adipose
3	chr2:190934600-190935000	Enhancers	HSMM	muscle
4	chr2:190934600-190935800	Enhancers	Liver	Liver
5	chr2:190934800-190935000	Enhancers	Fetal Muscle Leg	muscle

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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

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