Variant report

Variant	rs10520715
Chromosome Location	chr18:44713275-44713276
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44675483..44677024-chr18:44712613..44715236,2	K562	blood:
2	chr18:44711913..44713473-chr18:44718015..44720317,2	MCF-7	breast:
3	chr18:44626654..44628817-chr18:44712742..44715143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10083937	0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11082563	0.81[CHB][hapmap]
rs11082564	0.91[CHB][hapmap]
rs11082566	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11872531	0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11873315	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11873812	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11873880	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11874862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875768	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11876448	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11877644	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326221	0.83[ASN][1000 genomes]
rs12326412	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs12326457	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12326465	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12386092	0.81[CHB][hapmap]
rs12386097	0.80[AMR][1000 genomes]
rs13547	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1434528	0.91[CHB][hapmap];1.00[GIH][hapmap]
rs16948914	0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap]
rs16948928	0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap]
rs16949157	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16949275	0.90[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs16958432	1.00[GIH][hapmap];0.90[LWK][hapmap]
rs16958440	0.80[CHB][hapmap]
rs17711764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17712105	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712141	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712249	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17784795	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784867	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117373	0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap]
rs2289130	0.81[CHB][hapmap]
rs2289131	1.00[GIH][hapmap];0.90[LWK][hapmap]
rs2289132	0.85[GIH][hapmap]
rs28578518	0.83[ASN][1000 genomes]
rs28587821	0.83[ASN][1000 genomes]
rs3809965	0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809966	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs56395942	0.80[AMR][1000 genomes]
rs56654141	0.80[ASN][1000 genomes]
rs57744138	0.86[ASN][1000 genomes]
rs58061761	0.83[ASN][1000 genomes]
rs58715341	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59217333	0.83[ASN][1000 genomes]
rs60726022	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62095459	0.82[AMR][1000 genomes]
rs72907280	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72909237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909248	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998818	1.00[GIH][hapmap]

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	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
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10520715	HDHD2	cis	multi-tissue	Pritchard
rs10520715	IER3IP1	cis	cerebellum	SCAN
rs10520715	HDHD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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