Variant report

Variant	rs2717068
Chromosome Location	chr2:58094873-58094874
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58094285..58096431-chr2:58101485..58103642,2	MCF-7	breast:
2	chr2:58092863..58095736-chr2:58103912..58105798,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1040224	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs1040225	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10445894	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10496078	0.85[EUR][1000 genomes]
rs10496079	0.84[EUR][1000 genomes]
rs10865304	0.85[EUR][1000 genomes]
rs1106302	0.89[JPT][hapmap]
rs11898858	0.86[EUR][1000 genomes]
rs12713358	0.86[EUR][1000 genomes]
rs12713370	0.96[CEU][hapmap]
rs12990792	0.85[EUR][1000 genomes]
rs12997222	0.82[EUR][1000 genomes]
rs1356544	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1356545	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1401100	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1402398	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1518393	0.86[EUR][1000 genomes]
rs1518394	0.86[EUR][1000 genomes]
rs1518395	1.00[CEU][hapmap]
rs1568253	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1568254	0.87[EUR][1000 genomes]
rs1568450	0.87[EUR][1000 genomes]
rs1589407	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2090793	0.87[EUR][1000 genomes]
rs2139053	0.82[EUR][1000 genomes]
rs2139054	0.89[EUR][1000 genomes]
rs2176546	0.85[EUR][1000 genomes]
rs2204019	0.81[AMR][1000 genomes]
rs2312141	0.89[EUR][1000 genomes]
rs2312147	0.96[CEU][hapmap]
rs2465804	0.89[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678870	0.86[CEU][hapmap]
rs2678880	0.92[CEU][hapmap]
rs2678881	0.93[EUR][1000 genomes]
rs2678889	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2678890	0.87[EUR][1000 genomes]
rs2678891	0.87[EUR][1000 genomes]
rs2678896	0.87[EUR][1000 genomes]
rs2678897	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2678901	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2678903	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs2678904	0.91[EUR][1000 genomes]
rs2678905	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678906	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs2678908	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2678910	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2678915	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2683614	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683616	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683619	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683620	0.87[EUR][1000 genomes]
rs2683622	0.84[AMR][1000 genomes]
rs2683625	0.80[ASN][1000 genomes]
rs2683628	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683629	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2683634	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2716998	0.83[AMR][1000 genomes]
rs2716999	0.81[AMR][1000 genomes]
rs2717001	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2717002	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2717003	0.83[EUR][1000 genomes]
rs2717004	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2717006	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2717007	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2717015	0.89[EUR][1000 genomes]
rs2717018	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2717019	0.86[CEU][hapmap]
rs2717023	0.89[CEU][hapmap]
rs2717024	0.89[CEU][hapmap]
rs2717027	0.81[EUR][1000 genomes]
rs2717031	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2717032	0.87[EUR][1000 genomes]
rs2717035	0.87[EUR][1000 genomes]
rs2717036	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2717040	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2717041	0.85[EUR][1000 genomes]
rs2717043	0.86[CEU][hapmap]
rs2717048	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2717056	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2717063	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2717070	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2717072	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2717075	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28718871	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2953437	0.84[AMR][1000 genomes]
rs2953438	0.84[AMR][1000 genomes]
rs2953439	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2953441	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2953443	0.80[ASN][1000 genomes]
rs4672223	0.87[EUR][1000 genomes]
rs6545663	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6545664	0.87[EUR][1000 genomes]
rs6545665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6545677	0.93[CEU][hapmap]
rs66490669	0.82[AMR][1000 genomes]
rs66985942	0.80[AMR][1000 genomes]
rs6730037	0.86[EUR][1000 genomes]
rs6732310	1.00[CEU][hapmap]
rs6737913	0.85[EUR][1000 genomes]
rs6756221	0.87[EUR][1000 genomes]
rs6761347	0.87[EUR][1000 genomes]
rs7561842	0.85[EUR][1000 genomes]
rs7588492	0.83[EUR][1000 genomes]
rs7598169	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs970941	0.83[CEU][hapmap];0.87[EUR][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	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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
5	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

Variant related diseases (count:1)

Disease	PMID	Source
Epilepsy (generalized)	22949513	GWAS catalog

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58090200-58104200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:58092800-58095000	Weak transcription	A549	lung
3	chr2:58094800-58097400	Enhancers	Muscle Satellite Cultured Cells	--

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