Variant report

Variant	rs1486239
Chromosome Location	chr2:180631925-180631926
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10168253	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10182519	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930886	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11673837	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12693205	0.80[ASN][1000 genomes]
rs2615366	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs356412	0.81[ASN][1000 genomes]
rs357704	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603724	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4893881	0.90[ASN][1000 genomes]
rs55924451	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs723356	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs723357	0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1486239	HOXD11	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180629600-180633200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:180630000-180632200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:180630000-180632200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:180630200-180632200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr2:180630800-180633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:180631000-180632000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:180631000-180633200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:180631200-180632200	Strong transcription	Liver	Liver
9	chr2:180631600-180632000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:180631600-180632200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:180631800-180632000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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