Variant report

Variant	rs17039564
Chromosome Location	chr2:50186504-50186505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12621581	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12998574	0.91[JPT][hapmap]
rs1363046	0.92[CEU][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1421586	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421594	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1592729	0.87[JPT][hapmap]
rs17039529	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17039573	0.96[CEU][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17039575	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17039577	0.92[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17039582	0.92[CEU][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17439140	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs17491776	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2193868	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2351145	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4461296	0.87[JPT][hapmap]
rs56325957	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59672611	0.85[EUR][1000 genomes]
rs59973985	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713560	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6713940	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs725323	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7573698	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7574241	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9679140	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs983094	0.96[CEU][hapmap];0.86[EUR][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

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50141600-50187400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:50176200-50186600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:50178400-50186600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:50184200-50189000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:50185200-50188800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:50185600-50187200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:50185800-50188200	Weak transcription	Fetal Brain Male	brain
8	chr2:50186200-50187600	Enhancers	Fetal Brain Female	brain
9	chr2:50186400-50186600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:50186400-50186800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:50186400-50187600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr2:50186400-50188000	Enhancers	Brain Cingulate Gyrus	brain
13	chr2:50186400-50188600	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links