Variant report

Variant	rs12029858
Chromosome Location	chr1:70926930-70926931
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10458561	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889871	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145919	0.82[EUR][1000 genomes]
rs11590089	0.86[EUR][1000 genomes]
rs1960400	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967189	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650051	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473334	0.82[EUR][1000 genomes]
rs577476	0.81[EUR][1000 genomes]
rs583316	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58977414	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs663649	0.82[EUR][1000 genomes]
rs9633291	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1002709	chr1:70916210-70939526	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12029858	CTH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:70924400-70932000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:70925000-70927200	Enhancers	K562	blood
4	chr1:70925400-70927800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:70926000-70927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:70926000-70927200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:70926000-70928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:70926000-70928600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:70926400-70927200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:70926800-70927200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:70926800-70927600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:70926800-70928600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:70926800-70932000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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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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