Variant report

Variant	rs6131222
Chromosome Location	chr20:11479391-11479392
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11700189	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207910	0.94[ASN][1000 genomes]
rs2207911	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2423554	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876228	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6040739	0.96[ASN][1000 genomes]
rs6074301	0.94[ASN][1000 genomes]
rs6078190	0.95[ASN][1000 genomes]
rs6078204	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6104763	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6108906	0.86[JPT][hapmap]
rs6108988	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6108990	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134272	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134277	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs728487	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8123803	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973970	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1058734	chr20:11389232-11479953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv522929	chr20:11411026-11516418	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6131222	HAO1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11472400-11479600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11474000-11479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:11474000-11479600	Weak transcription	HMEC	breast
4	chr20:11474000-11479600	Weak transcription	NHEK	skin
5	chr20:11476400-11481000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:11477400-11479400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:11477400-11485600	Weak transcription	A549	lung
8	chr20:11478200-11483800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr20:11478400-11479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:11478800-11479400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr20:11478800-11479800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:11479000-11481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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

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