Variant report

Variant	rs827589
Chromosome Location	chr8:104363670-104363671
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104357721..104360271-chr8:104361773..104363841,2	MCF-7	breast:
2	chr8:104363177..104365270-chr8:104368358..104371064,2	MCF-7	breast:
3	chr8:104341563..104343824-chr8:104362835..104365347,2	MCF-7	breast:
4	chr8:104361320..104364178-chr8:104414745..104417725,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164933	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12680121	1.00[CEU][hapmap]
rs1610204	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs16870349	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[AMR][1000 genomes]
rs17207827	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs17228576	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs17228841	0.83[AMR][1000 genomes]
rs17801975	0.94[AMR][1000 genomes]
rs17802011	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[AMR][1000 genomes]
rs17802089	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17803441	1.00[GIH][hapmap];0.83[AMR][1000 genomes]
rs2687347	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs2687355	0.94[AMR][1000 genomes]
rs2687356	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2687367	1.00[CEU][hapmap]
rs2917546	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2917547	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2917548	1.00[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs2934725	0.94[AMR][1000 genomes]
rs3098226	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs3098234	0.83[AMR][1000 genomes]
rs3098235	0.83[AMR][1000 genomes]
rs3098238	0.83[AMR][1000 genomes]
rs3098239	0.83[AMR][1000 genomes]
rs3134252	0.83[AMR][1000 genomes]
rs3134257	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs3134260	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs3134269	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs3134284	0.83[AMR][1000 genomes]
rs3134294	0.83[AMR][1000 genomes]
rs6468868	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs7005750	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs703808	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs703809	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs71503493	0.81[AMR][1000 genomes]
rs73286089	0.83[AMR][1000 genomes]
rs73286092	0.83[AMR][1000 genomes]
rs73286095	0.83[AMR][1000 genomes]
rs750509	0.83[AMR][1000 genomes]
rs751725	0.83[AMR][1000 genomes]
rs827525	0.89[AMR][1000 genomes]
rs827527	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs827529	0.89[AMR][1000 genomes]
rs827531	0.89[AMR][1000 genomes]
rs827542	1.00[CEU][hapmap]
rs827543	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs827544	1.00[CEU][hapmap]
rs827545	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[AMR][1000 genomes]
rs827548	0.84[AMR][1000 genomes]
rs827549	0.89[AMR][1000 genomes]
rs827551	0.89[AMR][1000 genomes]
rs827591	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827594	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs827600	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs861169	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1023181	chr8:104298542-104366365	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1016395	chr8:104327541-104473005	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1021345	chr8:104361854-104879684	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv1032085	chr8:104362187-104878345	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs827589	RIMS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104355800-104363800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:104357800-104383400	Weak transcription	Aorta	Aorta
3	chr8:104359000-104363800	Enhancers	Fetal Heart	heart
4	chr8:104360200-104365800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr8:104360400-104364200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr8:104361200-104364000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:104361400-104363800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:104361400-104365400	Weak transcription	Dnd41	blood
9	chr8:104361600-104365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:104361600-104365400	Weak transcription	Gastric	stomach
11	chr8:104362000-104365600	Weak transcription	Thymus	Thymus
12	chr8:104362600-104365800	Weak transcription	HSMM	muscle
13	chr8:104363000-104363800	Weak transcription	Fetal Thymus	thymus
14	chr8:104363000-104364000	Enhancers	Brain Germinal Matrix	brain
15	chr8:104363000-104364000	Enhancers	Fetal Stomach	stomach
16	chr8:104363000-104369200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:104363000-104371800	Weak transcription	HSMMtube	muscle
18	chr8:104363200-104363800	Weak transcription	Placenta	Placenta
19	chr8:104363200-104372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:104363400-104364000	Enhancers	Fetal Brain Female	brain
21	chr8:104363600-104363800	Enhancers	Fetal Brain Male	brain
22	chr8:104363600-104365000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr8:104363600-104369000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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