Variant report

Variant	rs1673394
Chromosome Location	chr8:110483706-110483707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110483442..110487678-chr8:110550408..110553451,5	MCF-7	breast:
2	chr8:110480733..110484366-chr8:110549857..110553138,3	MCF-7	breast:
3	chr8:110483309..110485365-chr8:110487237..110489170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147654	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1026439	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1457284	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471124	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1471125	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563579	0.81[ASN][1000 genomes]
rs1624114	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626759	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1627570	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673390	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673392	0.94[ASN][1000 genomes]
rs1673393	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673396	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673397	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673398	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673400	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673401	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673403	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673404	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1673405	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673407	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673408	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783142	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783143	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783144	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783145	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783149	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783150	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783152	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783163	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783164	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1783165	0.86[ASN][1000 genomes]
rs2607637	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607638	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607639	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844251	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844252	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844253	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7002606	0.80[EUR][1000 genomes]
rs714994	0.93[ASN][1000 genomes]
rs714995	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	nsv1018510	chr8:110403496-110504029	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv891281	chr8:110450092-110558622	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv981974	chr8:110482256-110484135	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1673394	PKHD1L1	cis	Nerve Tibial	GTEx
rs1673394	PKHD1L1	cis	multi-tissue	Pritchard
rs1673394	RP11-419L20.2	cis	Thyroid	GTEx
rs1673394	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1673394	PKHD1L1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110463200-110492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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