Variant report

Variant	rs5020729
Chromosome Location	chr1:180565758-180565759
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494530	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10737347	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10737348	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10753220	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753221	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798784	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3845403	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3845404	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856052	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3856055	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3915573	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4111062	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4111063	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4111064	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4144583	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7521872	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544326	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551817	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554099	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS 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 miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5020729	KIAA0241	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180563600-180567200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180564200-180567600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:180564400-180566200	Weak transcription	Fetal Brain Female	brain
4	chr1:180564400-180572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:180564600-180567200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180564800-180566400	Weak transcription	A549	lung
7	chr1:180564800-180567400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:180564800-180567400	Weak transcription	Pancreas	Pancrea
9	chr1:180564800-180567400	Weak transcription	K562	blood
10	chr1:180564800-180567600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:180564800-180567600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:180564800-180579600	Weak transcription	Right Atrium	heart
13	chr1:180565000-180567800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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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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