Variant report

Variant	rs9428896
Chromosome Location	chr1:241979567-241979568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241972366..241975039-chr1:241979342..241982449,3	MCF-7	breast:
2	chr1:241801647..241805071-chr1:241978967..241982321,4	MCF-7	breast:
3	chr1:241803378..241805709-chr1:241977902..241981601,4	MCF-7	breast:
4	chr1:241801162..241804735-chr1:241978255..241982638,4	K562	blood:
5	chr1:241961947..241964736-chr1:241977926..241980630,2	MCF-7	breast:
6	chr1:241975494..241979685-chr1:241981885..241985548,4	MCF-7	breast:
7	chr1:241976902..241978812-chr1:241979231..241982156,2	K562	blood:
8	chr1:241969994..241971972-chr1:241979527..241981528,2	MCF-7	breast:
9	chr1:241974667..241976775-chr1:241978284..241980984,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10047251	0.94[CEU][hapmap]
rs10489351	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10926555	0.87[JPT][hapmap]
rs10926568	0.94[CEU][hapmap]
rs10926572	0.94[CEU][hapmap]
rs10926574	0.93[CEU][hapmap]
rs12021981	0.89[ASN][1000 genomes]
rs12030185	0.93[ASN][1000 genomes]
rs12033730	0.86[JPT][hapmap]
rs12037438	0.98[ASN][1000 genomes]
rs12047688	0.98[ASN][1000 genomes]
rs12074374	0.94[CEU][hapmap]
rs12075350	0.94[CEU][hapmap]
rs12091633	0.93[CEU][hapmap]
rs12092046	0.88[CEU][hapmap]
rs12095445	0.94[CEU][hapmap]
rs13375989	0.94[CEU][hapmap]
rs1342867	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs4658798	1.00[CEU][hapmap]
rs6429298	0.94[CEU][hapmap]
rs6429299	0.94[CEU][hapmap]
rs6429302	0.94[CEU][hapmap]
rs6429311	0.94[CEU][hapmap]
rs6660576	0.94[CEU][hapmap]
rs6660686	0.94[CEU][hapmap]
rs6663895	0.94[CEU][hapmap]
rs6667772	0.93[CEU][hapmap]
rs6670605	0.94[CEU][hapmap]
rs6680528	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685969	0.93[CEU][hapmap]
rs6694094	0.91[CEU][hapmap]
rs6698158	0.94[CEU][hapmap]
rs6698460	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703922	0.92[CEU][hapmap]
rs7514880	0.94[CEU][hapmap]
rs7524386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533124	0.85[CEU][hapmap]
rs7539331	0.82[JPT][hapmap]
rs7552731	0.94[CEU][hapmap]
rs7554579	0.94[CEU][hapmap]
rs851777	1.00[CEU][hapmap]
rs9428522	0.93[CEU][hapmap]
rs9428526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9428897	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9428896	SDCCAG8	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241976600-241981000	Weak transcription	Aorta	Aorta
2	chr1:241976600-241981400	Weak transcription	K562	blood
3	chr1:241977200-241980200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:241977400-241981800	Enhancers	Hela-S3	cervix
5	chr1:241977600-241980200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:241978200-241980200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:241978400-241980000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:241978600-241980000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:241979400-241980200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:241979400-241982000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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