Variant report

Variant	rs2678906
Chromosome Location	chr2:58134048-58134049
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:58132313-58134173	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58133060..58135151-chr2:58272508..58275235,2	MCF-7	breast:
2	chr2:58133863..58138456-chr2:58272095..58275151,4	MCF-7	breast:

Variant related genes	Relation type
VRK2	TF binding region
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10188070	0.94[JPT][hapmap]
rs1040224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10496078	0.81[EUR][1000 genomes]
rs10496079	0.81[EUR][1000 genomes]
rs10865304	0.81[EUR][1000 genomes]
rs11898858	0.82[EUR][1000 genomes]
rs12622856	0.84[JPT][hapmap]
rs12713358	0.82[EUR][1000 genomes]
rs12713370	0.93[CEU][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12990792	0.81[EUR][1000 genomes]
rs1356544	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1356545	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1401100	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1402398	0.84[EUR][1000 genomes]
rs1518393	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1518394	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1518395	0.92[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1518399	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1568252	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1568253	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1568254	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568450	0.83[EUR][1000 genomes]
rs1589407	0.84[EUR][1000 genomes]
rs2090793	0.84[EUR][1000 genomes]
rs2139053	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2139054	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176546	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312141	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312147	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2465804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2678880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2678881	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2678889	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678890	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678891	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678896	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678897	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678904	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678910	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2678915	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2683614	0.84[EUR][1000 genomes]
rs2683616	0.84[EUR][1000 genomes]
rs2683619	0.84[EUR][1000 genomes]
rs2683620	0.84[EUR][1000 genomes]
rs2683628	0.84[EUR][1000 genomes]
rs2683629	0.84[EUR][1000 genomes]
rs2683634	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2717001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2717002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2717003	0.90[EUR][1000 genomes]
rs2717004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2717006	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2717007	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2717015	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717018	0.84[EUR][1000 genomes]
rs2717019	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2717023	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2717024	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2717027	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2717031	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717032	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717035	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717036	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717040	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2717041	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2717043	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2717048	0.83[EUR][1000 genomes]
rs2717056	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2717063	0.93[EUR][1000 genomes]
rs2717068	0.93[EUR][1000 genomes]
rs2717075	0.84[EUR][1000 genomes]
rs28718871	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2953439	0.83[EUR][1000 genomes]
rs2953441	0.84[EUR][1000 genomes]
rs4672223	0.84[EUR][1000 genomes]
rs6545663	0.84[EUR][1000 genomes]
rs6545664	0.84[EUR][1000 genomes]
rs6545665	0.84[EUR][1000 genomes]
rs6545677	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6730037	0.82[EUR][1000 genomes]
rs6732310	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6737913	0.81[EUR][1000 genomes]
rs6756221	0.83[EUR][1000 genomes]
rs6761347	0.83[EUR][1000 genomes]
rs7561842	0.81[EUR][1000 genomes]
rs7598169	0.84[EUR][1000 genomes]
rs908730	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs970941	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58132400-58135000	Enhancers	A549	lung
2	chr2:58133200-58134400	Enhancers	Brain Hippocampus Middle	brain
3	chr2:58133600-58136200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr2:58133800-58134200	Enhancers	Brain Anterior Caudate	brain
5	chr2:58133800-58138400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:58134000-58134800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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