Variant report

Variant	rs17712105
Chromosome Location	chr18:44734565-44734566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10083937	0.80[ASN][1000 genomes]
rs10520715	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11082566	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872531	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11873315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873812	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873880	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11874862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11875558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11875768	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11876448	0.82[AMR][1000 genomes]
rs11877644	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11877745	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12326221	0.80[ASN][1000 genomes]
rs12326412	0.80[ASN][1000 genomes]
rs12326457	0.80[ASN][1000 genomes]
rs12326465	0.80[ASN][1000 genomes]
rs12386097	0.80[AMR][1000 genomes]
rs13547	0.82[AMR][1000 genomes]
rs16949157	0.80[ASN][1000 genomes]
rs16949275	0.83[ASN][1000 genomes]
rs17711764	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17712249	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784414	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17784795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578518	0.80[ASN][1000 genomes]
rs28587821	0.80[ASN][1000 genomes]
rs3809965	0.80[ASN][1000 genomes]
rs3809966	0.80[ASN][1000 genomes]
rs56395942	0.80[AMR][1000 genomes]
rs57744138	0.83[ASN][1000 genomes]
rs58061761	0.80[ASN][1000 genomes]
rs58715341	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59217333	0.80[ASN][1000 genomes]
rs60726022	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62095459	0.82[AMR][1000 genomes]
rs72907280	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72909237	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72909248	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17712105	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44729800-44736600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr18:44732600-44734600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:44733200-44736000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:44733800-44736000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr18:44734000-44736200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr18:44734200-44736200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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