Variant report

Variant	rs2980585
Chromosome Location	chr8:110360528-110360529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110358764..110360570-chr8:110733520..110735088,2	MCF-7	breast:
2	chr8:110359161..110361961-chr8:110559520..110561613,2	MCF-7	breast:
3	chr4:128981488..128983181-chr8:110359982..110361978,2	MCF-7	breast:
4	chr8:110356952..110358938-chr8:110359155..110360701,2	K562	blood:
5	chr8:110345281..110347991-chr8:110360472..110362905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120526	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000120533	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10092693	0.83[YRI][hapmap]
rs10097258	0.83[YRI][hapmap]
rs10101522	0.82[YRI][hapmap]
rs10955518	0.83[YRI][hapmap]
rs11998321	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12164209	0.90[YRI][hapmap]
rs12546429	0.83[YRI][hapmap]
rs12679728	0.83[YRI][hapmap]
rs12680439	0.83[YRI][hapmap]
rs13252234	0.83[YRI][hapmap]
rs13253951	0.83[YRI][hapmap]
rs13254245	0.83[YRI][hapmap]
rs13254461	0.83[YRI][hapmap]
rs13258279	0.83[YRI][hapmap]
rs13262995	0.83[YRI][hapmap]
rs13266374	0.83[YRI][hapmap]
rs13439864	0.91[CEU][hapmap]
rs1379363	0.83[YRI][hapmap]
rs1379364	0.83[YRI][hapmap]
rs1457292	0.83[YRI][hapmap]
rs1458920	0.83[YRI][hapmap]
rs16879547	0.89[YRI][hapmap]
rs1824193	0.83[YRI][hapmap]
rs1870108	0.83[YRI][hapmap]
rs1870389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2124982	0.83[YRI][hapmap]
rs2349436	0.83[YRI][hapmap]
rs2349761	0.83[YRI][hapmap]
rs2926229	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926230	0.82[ASN][1000 genomes]
rs2926232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926233	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926234	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2926237	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926239	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926242	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980570	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980586	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734212	0.83[YRI][hapmap]
rs4735134	0.83[YRI][hapmap]
rs6993552	0.83[YRI][hapmap]
rs7014589	0.91[YRI][hapmap]
rs7016085	0.83[YRI][hapmap]
rs7016609	0.83[YRI][hapmap]
rs7819141	0.83[YRI][hapmap]
rs897839	0.83[YRI][hapmap]
rs921958	0.83[YRI][hapmap]
rs921959	0.83[YRI][hapmap]
rs9297425	0.83[YRI][hapmap]
rs9642806	0.83[YRI][hapmap]
rs9643050	0.81[YRI][hapmap]
rs964307	0.83[YRI][hapmap]
rs9656793	0.83[YRI][hapmap]
rs9656882	0.83[YRI][hapmap]
rs965930	0.83[YRI][hapmap]

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	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	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2980585	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2980585	PKHD1L1	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110348800-110364400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:110353000-110361600	Weak transcription	NHDF-Ad	bronchial
3	chr8:110357200-110360600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr8:110357200-110360600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr8:110357200-110360600	Weak transcription	K562	blood
6	chr8:110357400-110360600	Weak transcription	Brain Hippocampus Middle	brain
7	chr8:110357400-110360800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr8:110357400-110360800	Weak transcription	Fetal Intestine Large	intestine
9	chr8:110357400-110360800	Weak transcription	Left Ventricle	heart
10	chr8:110357600-110361400	Weak transcription	Primary B cells from peripheral blood	blood

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