Variant report

Variant	rs28260
Chromosome Location	chr7:117921267-117921268
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: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10247768	0.92[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs10487392	0.88[EUR][1000 genomes]
rs11487110	0.84[CEU][hapmap]
rs11542074	0.83[EUR][1000 genomes]
rs11974039	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs11983651	0.88[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs12112697	0.84[CEU][hapmap]
rs12154684	0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs1544583	0.88[EUR][1000 genomes]
rs1544584	0.82[EUR][1000 genomes]
rs17140984	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs17141053	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2041527	0.88[CEU][hapmap]
rs2215628	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2286863	0.83[EUR][1000 genomes]
rs2286865	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
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]
rs41925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs62466471	0.83[EUR][1000 genomes]
rs62466515	0.83[EUR][1000 genomes]
rs6960940	0.84[EUR][1000 genomes]
rs6964911	0.83[CEU][hapmap]
rs7786233	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7801976	0.94[EUR][1000 genomes]
rs881801	0.88[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
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	nsv889089	chr7:117865940-117921267	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28260	ANKRD7	cis	cerebellum	SCAN
rs28260	ANKRD7	cis	parietal	SCAN
rs28260	LSM8	cis	multi-tissue	Pritchard
rs28260	KCND2	cis	parietal	SCAN
rs28260	NAA38	cis	parietal	SCAN

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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