Variant report

Variant	rs10489252
Chromosome Location	chr1:171748145-171748146
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171715474..171717063-chr1:171747141..171749342,2	K562	blood:
2	chr1:171738907..171740950-chr1:171747822..171750244,2	MCF-7	breast:
3	chr1:171746858..171748372-chr1:171748853..171751746,3	K562	blood:
4	chr1:171734034..171736178-chr1:171746102..171748315,3	K562	blood:
5	chr1:171709792..171712103-chr1:171746642..171748516,2	K562	blood:
6	chr1:171729687..171733295-chr1:171747531..171751881,5	K562	blood:
7	chr1:171738793..171742009-chr1:171745293..171748243,3	K562	blood:
8	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL13-3	chr1:171748117-171748192	NONHSAT007582

No data

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045456	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913683	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12091786	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565176	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17596025	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17596081	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17649609	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes]
rs17650310	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143369	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181216	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2223602	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2232807	0.82[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232813	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232819	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232825	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294718	1.00[CEU][hapmap]
rs236894	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs236907	1.00[CEU][hapmap]
rs34320898	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35400839	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35631282	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35674909	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35882887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35930163	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36080557	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3891278	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6675708	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681322	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7522582	0.94[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536142	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	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	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489252	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171740000-171749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:171745400-171749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:171747000-171749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:171747200-171748400	Weak transcription	K562	blood
5	chr1:171747200-171749400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:171747600-171749600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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