Variant report

Variant	rs17472925
Chromosome Location	chr1:171939952-171939953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10914141	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120554	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122025	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123334	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125022	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133814	0.80[EUR][1000 genomes]
rs12135615	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12135871	0.80[EUR][1000 genomes]
rs12137105	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12137824	0.80[EUR][1000 genomes]
rs12137825	0.80[EUR][1000 genomes]
rs12141726	0.82[EUR][1000 genomes]
rs12144607	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145177	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843855	1.00[JPT][hapmap]
rs16843860	1.00[JPT][hapmap]
rs17277008	1.00[JPT][hapmap]
rs17346438	1.00[JPT][hapmap]
rs17346452	1.00[JPT][hapmap]
rs17346473	1.00[JPT][hapmap]
rs17350544	1.00[JPT][hapmap]
rs17350579	1.00[JPT][hapmap]
rs17350586	1.00[JPT][hapmap]
rs17361789	1.00[JPT][hapmap]
rs4540689	1.00[JPT][hapmap]
rs61805807	0.80[EUR][1000 genomes]
rs61805811	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61805813	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61805815	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61805816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61805845	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673009	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs6684723	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691703	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694089	1.00[JPT][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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17472925	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171936600-171948600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:171937200-171942000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:171937400-171958000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:171937800-171947400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:171938600-171941000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:171939000-171940200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:171939000-171941200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:171939000-171941400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:171939200-171940200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:171939200-171940400	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:171939200-171940400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:171939200-171941000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:171939200-171941400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:171939600-171941200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:171939800-171940000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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