Variant report

Variant	rs2945880
Chromosome Location	chr8:8254590-8254591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8242139..8245005-chr8:8252553..8254916,3	MCF-7	breast:
2	chr8:8153909..8155842-chr8:8254348..8256276,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2920988	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2920989	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2945872	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2945877	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945878	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2976916	0.89[EUR][1000 genomes]
rs2976925	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2976932	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2979136	1.00[JPT][hapmap]
rs2979145	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6601695	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817196	chr8:8079861-8255544	Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1020290	chr8:8108863-8260280	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
8	nsv539440	chr8:8108863-8260280	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
16	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
17	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2945880	AGPAT5	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8245000-8255600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:8245000-8256800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:8248600-8256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:8249000-8266200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:8249200-8255400	Weak transcription	HepG2	liver
6	chr8:8249400-8254600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:8249400-8254800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:8249800-8255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:8252800-8256200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr8:8252800-8256400	Weak transcription	Osteobl	bone
11	chr8:8253200-8260200	Weak transcription	HSMMtube	muscle
12	chr8:8253800-8256600	Enhancers	Primary B cells from cord blood	blood
13	chr8:8253800-8257200	Enhancers	Primary B cells from peripheral blood	blood
14	chr8:8254000-8256400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr8:8254000-8257200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:8254000-8257800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr8:8254200-8254600	Enhancers	Brain Germinal Matrix	brain
18	chr8:8254200-8254800	Enhancers	Fetal Lung	lung
19	chr8:8254200-8254800	Flanking Active TSS	GM12878-XiMat	blood
20	chr8:8254200-8256400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:8254200-8256600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:8254200-8257200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr8:8254200-8257400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr8:8254200-8258200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr8:8254400-8254800	Enhancers	Fetal Kidney	kidney
26	chr8:8254400-8255000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr8:8254400-8255400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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