Variant report

Variant	rs2717006
Chromosome Location	chr2:58146956-58146957
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10188070	0.94[JPT][hapmap]
rs1040224	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1040225	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12622856	0.84[JPT][hapmap]
rs12713370	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1356544	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1356545	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1401100	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1518393	0.81[ASN][1000 genomes]
rs1518394	0.84[ASN][1000 genomes]
rs1518395	1.00[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1518399	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1568252	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1568253	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1568254	0.82[ASN][1000 genomes]
rs2139053	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139054	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2176546	0.87[ASN][1000 genomes]
rs2312141	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2312147	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2465804	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678870	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2678880	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2678881	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2678889	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2678890	0.82[ASN][1000 genomes]
rs2678891	0.82[ASN][1000 genomes]
rs2678896	0.82[ASN][1000 genomes]
rs2678897	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2678901	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678903	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678904	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678905	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2678906	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2678908	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2678910	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2678915	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683634	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2717001	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2717002	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2717004	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717007	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2717015	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2717019	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2717023	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2717024	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2717027	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2717031	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2717032	0.82[ASN][1000 genomes]
rs2717035	0.81[ASN][1000 genomes]
rs2717036	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2717040	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2717041	0.83[ASN][1000 genomes]
rs2717043	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2717056	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2717063	0.80[EUR][1000 genomes]
rs2717068	0.84[EUR][1000 genomes]
rs28718871	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545677	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66490669	0.81[EUR][1000 genomes]
rs6732310	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs966721	0.81[EUR][1000 genomes]
rs970941	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv874199	chr2:58031249-58161520	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58137800-58148000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:58139200-58147800	Weak transcription	Brain Substantia Nigra	brain
3	chr2:58146200-58148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:58146400-58147400	Weak transcription	Fetal Brain Male	brain
5	chr2:58146800-58148400	Enhancers	Brain Germinal Matrix	brain

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