Variant report

Variant	rs41925
Chromosome Location	chr7:117921372-117921373
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	chr7:117916864..117919001-chr7:117920265..117922583,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10247768	0.83[EUR][1000 genomes]
rs10487392	0.88[EUR][1000 genomes]
rs11542074	0.83[EUR][1000 genomes]
rs12154684	0.80[EUR][1000 genomes]
rs1544583	0.88[EUR][1000 genomes]
rs1544584	0.82[EUR][1000 genomes]
rs17140984	0.82[EUR][1000 genomes]
rs17141053	0.82[EUR][1000 genomes]
rs2215628	0.83[EUR][1000 genomes]
rs2286863	0.83[EUR][1000 genomes]
rs28260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33924981	0.83[EUR][1000 genomes]
rs34019303	0.83[EUR][1000 genomes]
rs35218902	0.84[EUR][1000 genomes]
rs35485182	0.80[EUR][1000 genomes]
rs41903	0.90[EUR][1000 genomes]
rs41904	0.90[EUR][1000 genomes]
rs41908	0.80[EUR][1000 genomes]
rs41912	0.92[EUR][1000 genomes]
rs41921	0.94[EUR][1000 genomes]
rs41923	0.94[EUR][1000 genomes]
rs41924	0.94[EUR][1000 genomes]
rs41930	0.89[EUR][1000 genomes]
rs41931	0.91[EUR][1000 genomes]
rs41936	0.90[EUR][1000 genomes]
rs41962	0.86[EUR][1000 genomes]
rs41989	0.86[EUR][1000 genomes]
rs4260839	0.83[EUR][1000 genomes]
rs45604739	0.83[EUR][1000 genomes]
rs4730837	0.82[EUR][1000 genomes]
rs62466471	0.83[EUR][1000 genomes]
rs62466515	0.83[EUR][1000 genomes]
rs6960940	0.84[EUR][1000 genomes]
rs7786233	0.81[EUR][1000 genomes]
rs7801976	0.94[EUR][1000 genomes]
rs9641593	0.82[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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889090	chr7:117865940-118067460	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv889091	chr7:117899190-117963926	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1029103	chr7:117917362-118035987	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2764014	chr7:117917374-118035999	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv608261	chr7:117917719-117965390	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv518701	chr7:117921267-117928764	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3350080	chr7:117921328-117921626	Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41925	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117919600-117922600	Enhancers	Dnd41	blood
2	chr7:117920200-117921400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:117920200-117921600	Enhancers	Fetal Intestine Small	intestine
4	chr7:117921000-117921800	Enhancers	Duodenum Mucosa	Duodenum
5	chr7:117921000-117922000	Enhancers	HUVEC	blood vessel
6	chr7:117921200-117921600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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