Variant report

Variant	rs10254954
Chromosome Location	chr7:40552023-40552024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1000013	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1019018	0.84[EUR][1000 genomes]
rs10263677	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10429076	0.86[AFR][1000 genomes]
rs10486810	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10486811	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs11973006	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs11974322	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11977013	0.82[YRI][hapmap]
rs11980464	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11982075	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17171727	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17171730	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17171734	0.86[EUR][1000 genomes]
rs1859660	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2329818	0.81[EUR][1000 genomes]
rs2329819	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28657711	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34523428	0.82[EUR][1000 genomes]
rs3919491	0.84[EUR][1000 genomes]
rs4720367	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4720368	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4720370	0.81[EUR][1000 genomes]
rs4720371	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4723966	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4723967	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723968	0.95[EUR][1000 genomes]
rs4723969	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4723970	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4723972	0.84[EUR][1000 genomes]
rs57268522	0.93[EUR][1000 genomes]
rs60011074	0.86[EUR][1000 genomes]
rs60999211	0.84[EUR][1000 genomes]
rs6462985	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6943787	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6945570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948724	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6956277	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs6977104	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73308254	0.95[EUR][1000 genomes]
rs73308257	0.95[EUR][1000 genomes]
rs73308260	0.91[EUR][1000 genomes]
rs73308263	0.91[EUR][1000 genomes]
rs73308264	0.88[EUR][1000 genomes]
rs73308269	0.87[EUR][1000 genomes]
rs73308281	0.85[EUR][1000 genomes]
rs73308284	0.86[EUR][1000 genomes]
rs73308289	0.88[EUR][1000 genomes]
rs73308291	0.84[EUR][1000 genomes]
rs73308300	0.84[EUR][1000 genomes]
rs73310208	0.81[EUR][1000 genomes]
rs7776976	0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7808612	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs917204	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv817404	chr7:40295934-40573605	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830969	chr7:40422576-40582389	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1017615	chr7:40445480-40570791	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1030515	chr7:40501867-40634808	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv830971	chr7:40523075-40700172	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40534000-40558600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:40549600-40552800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:40551200-40552200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:40552000-40552200	Active TSS	Aorta	Aorta

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