Variant report

Variant	rs1563579
Chromosome Location	chr8:110462358-110462359
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	chr8:110462238..110464562-chr8:110469589..110471882,2	K562	blood:
2	chr8:110461291..110465454-chr8:110550197..110554392,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147654	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1026439	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12334438	0.80[CHB][hapmap]
rs1379369	0.80[CHB][hapmap]
rs1379370	0.80[CHB][hapmap]
rs1457284	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1457289	0.80[CHB][hapmap]
rs1471124	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1471125	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1624114	0.86[ASN][1000 genomes]
rs1626759	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1627570	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1673390	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1673393	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1673394	0.81[ASN][1000 genomes]
rs1673396	0.96[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673397	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1673398	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1673400	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673401	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1673403	0.83[ASN][1000 genomes]
rs1673404	0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1673405	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1673407	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1673408	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1783142	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1783143	0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1783144	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1783145	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1783149	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs1783151	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs1783152	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1783163	0.92[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1783164	0.87[ASN][1000 genomes]
rs1783165	0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1870107	0.82[ASN][1000 genomes]
rs2349760	0.80[CHB][hapmap]
rs2607637	0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2607638	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2607639	0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2844232	0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs2844251	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2844252	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2844253	0.92[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2926236	1.00[YRI][hapmap]
rs2980639	0.88[YRI][hapmap]
rs4735133	0.80[ASN][1000 genomes]
rs6469261	0.85[CEU][hapmap]
rs6469262	0.83[CEU][hapmap]
rs7002606	0.81[JPT][hapmap]
rs714994	0.87[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs714995	0.83[ASN][1000 genomes]
rs9297426	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891280	chr8:110346363-110465481	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1563579	PKHD1L1	cis	Lymphoblastoid	GTEx
rs1563579	PKHD1L1	cis	Nerve Tibial	GTEx
rs1563579	RP11-419L20.2	cis	Thyroid	GTEx
rs1563579	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1563579	PKHD1L1	cis	multi-tissue	Pritchard
rs1563579	PKHD1L1	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110455600-110463000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:110457800-110462800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:110457800-110462800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr8:110459400-110462800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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