Variant report

Variant	rs4342559
Chromosome Location	chr8:110126285-110126286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:110123945..110126295-chr8:110127481..110129348,2	MCF-7	breast:
2	chr1:117352800..117353337-chr8:110126161..110126984,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10086023	0.85[ASN][1000 genomes]
rs10090944	0.85[ASN][1000 genomes]
rs10098145	0.85[ASN][1000 genomes]
rs10505126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785269	0.87[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs12543246	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544197	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs12544462	0.84[ASN][1000 genomes]
rs12679311	0.85[ASN][1000 genomes]
rs12680028	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13254233	0.84[ASN][1000 genomes]
rs13269597	0.85[ASN][1000 genomes]
rs1380096	0.87[JPT][hapmap]
rs1380097	0.87[JPT][hapmap]
rs1458915	0.87[JPT][hapmap]
rs1458916	0.87[JPT][hapmap]
rs1458917	0.87[JPT][hapmap]
rs1548082	0.91[JPT][hapmap]
rs1548083	0.91[JPT][hapmap]
rs16892486	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs16892496	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2926198	0.87[JPT][hapmap]
rs2980603	0.87[JPT][hapmap]
rs2980618	0.95[JPT][hapmap]
rs2980624	0.87[JPT][hapmap]
rs34092076	0.83[ASN][1000 genomes]
rs3925087	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3925088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4130682	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4236801	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4236802	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4446710	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4464939	0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4546626	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4734190	0.86[ASN][1000 genomes]
rs4734192	0.85[ASN][1000 genomes]
rs4734193	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4734194	0.83[ASN][1000 genomes]
rs4734195	0.83[ASN][1000 genomes]
rs4735091	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4735092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4735093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4735094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4735095	0.85[ASN][1000 genomes]
rs4735096	0.80[ASN][1000 genomes]
rs5778	0.86[ASN][1000 genomes]
rs6469235	0.85[ASN][1000 genomes]
rs6469241	0.83[ASN][1000 genomes]
rs6996836	0.81[ASN][1000 genomes]
rs7821463	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7823804	0.88[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs7828207	0.88[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs7832552	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7840000	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7844643	0.88[CHB][hapmap];0.96[JPT][hapmap];0.86[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	nsv1022273	chr8:110026712-110146600	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv539715	chr8:110026712-110146600	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4342559	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs4342559	PKHD1L1	cis	multi-tissue	Pritchard
rs4342559	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110121400-110144600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:110124400-110130200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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