Variant report

Variant	rs6888146
Chromosome Location	chr5:43225436-43225437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43121173..43123733-chr5:43225214..43227134,2	MCF-7	breast:
2	chr5:43120976..43123140-chr5:43225337..43226938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1050336	1.00[AMR][1000 genomes]
rs10805669	0.98[AFR][1000 genomes]
rs1690989	1.00[AMR][1000 genomes]
rs1690996	1.00[AMR][1000 genomes]
rs2444778	1.00[AMR][1000 genomes]
rs2453311	1.00[AMR][1000 genomes]
rs4473775	0.98[AFR][1000 genomes]
rs4533896	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs4549536	1.00[AMR][1000 genomes]
rs4588602	0.98[AFR][1000 genomes]
rs473870	1.00[AMR][1000 genomes]
rs481347	1.00[AMR][1000 genomes]
rs482224	1.00[AMR][1000 genomes]
rs4866730	0.93[AFR][1000 genomes]
rs4866731	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs500322	1.00[AMR][1000 genomes]
rs500993	1.00[AMR][1000 genomes]
rs516939	1.00[AMR][1000 genomes]
rs534655	1.00[AMR][1000 genomes]
rs549343	1.00[AMR][1000 genomes]
rs550847	1.00[AMR][1000 genomes]
rs558935	1.00[AMR][1000 genomes]
rs566582	1.00[AMR][1000 genomes]
rs623083	1.00[AMR][1000 genomes]
rs6414901	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6451679	0.98[AFR][1000 genomes]
rs661413	1.00[AMR][1000 genomes]
rs665790	1.00[AMR][1000 genomes]
rs666663	1.00[AMR][1000 genomes]
rs6859969	0.85[YRI][hapmap]
rs6863940	1.00[AMR][1000 genomes]
rs693466	1.00[AMR][1000 genomes]
rs7712183	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7727600	0.87[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7730565	1.00[AMR][1000 genomes]
rs782973	1.00[AMR][1000 genomes]
rs782981	1.00[AMR][1000 genomes]
rs782982	1.00[AMR][1000 genomes]
rs782983	1.00[AMR][1000 genomes]
rs782986	1.00[AMR][1000 genomes]
rs803501	1.00[AMR][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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 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	chr5:43196200-43245400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:43209600-43245200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:43215600-43236800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43219000-43226000	Weak transcription	Brain Angular Gyrus	brain
5	chr5:43219200-43232000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:43225200-43226600	Enhancers	Thymus	Thymus

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