Variant report

Variant	rs16868401
Chromosome Location	chr5:89560757-89560758
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89431318..89432484-chr5:89560747..89561819,9	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16868382	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868390	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868392	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868393	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868395	0.98[AFR][1000 genomes]
rs16868397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868404	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16868414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2916623	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs57348675	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59769329	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6864615	1.00[AMR][1000 genomes]
rs73184878	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184879	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184884	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184886	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184891	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73184895	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73186611	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73186617	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv882362	chr5:89437963-89604380	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830391	chr5:89456582-89641195	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv830393	chr5:89499644-89658493	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89529800-89560800	Weak transcription	Aorta	Aorta
2	chr5:89558200-89560800	Enhancers	Fetal Brain Male	brain
3	chr5:89559000-89561200	Enhancers	Fetal Brain Female	brain
4	chr5:89559200-89560800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:89559600-89561200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:89559800-89560800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:89560000-89561200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:89560400-89561000	Enhancers	HSMM	muscle
9	chr5:89560600-89561000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:89560600-89561000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:89560600-89561200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:89560600-89561200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:89560600-89561200	Enhancers	Primary B cells from cord blood	blood
14	chr5:89560600-89561200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:89560600-89561200	Active TSS	Brain Germinal Matrix	brain
16	chr5:89560600-89561200	Enhancers	GM12878-XiMat	blood
17	chr5:89560600-89561200	Enhancers	NHDF-Ad	bronchial
18	chr5:89560600-89561400	Enhancers	Primary B cells from peripheral blood	blood

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