Variant report

Variant	rs17439140
Chromosome Location	chr2:50195048-50195049
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1013597	0.81[JPT][hapmap]
rs11125278	0.81[JPT][hapmap]
rs11885824	0.85[JPT][hapmap]
rs11902804	0.81[JPT][hapmap]
rs12617277	0.85[JPT][hapmap]
rs12621581	1.00[CEU][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13007882	0.85[JPT][hapmap]
rs13016321	0.81[JPT][hapmap]
rs13022108	0.81[JPT][hapmap]
rs1363046	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1421586	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1421594	1.00[CEU][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs17039456	0.81[JPT][hapmap]
rs17039472	0.81[JPT][hapmap]
rs17039484	0.85[JPT][hapmap]
rs17039508	0.81[JPT][hapmap]
rs17039529	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs17039564	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs17039573	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17039575	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs17039577	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs17039582	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs17491776	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17491881	0.93[YRI][hapmap]
rs2193868	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241750	0.85[JPT][hapmap]
rs2241752	0.81[JPT][hapmap]
rs4143112	0.85[JPT][hapmap]
rs56325957	0.81[EUR][1000 genomes]
rs59672611	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59973985	0.81[EUR][1000 genomes]
rs6713560	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6713940	0.95[CEU][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6758043	0.85[JPT][hapmap]
rs725323	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7573698	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7574241	1.00[CEU][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs7598993	0.81[JPT][hapmap]
rs920033	0.85[JPT][hapmap]
rs920035	0.85[JPT][hapmap]
rs9679140	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs983094	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932839	chr2:50181785-50225697	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17439140	MIR638	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50187600-50199800	Weak transcription	Fetal Brain Female	brain
2	chr2:50188000-50198200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:50188600-50199400	Weak transcription	Fetal Brain Male	brain
4	chr2:50188600-50199600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:50193400-50200600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:50193600-50199400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:50194000-50195200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:50194600-50195200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:50195000-50199400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:50195000-50199600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:50195000-50200000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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