Variant report

Variant	rs7309105
Chromosome Location	chr12:122321699-122321700
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122319850..122323065-chr12:122324628..122326672,4	MCF-7	breast:
2	chr12:122313122..122314664-chr12:122320554..122322412,2	K562	blood:
3	chr12:122239544..122241081-chr12:122321387..122323397,2	MCF-7	breast:
4	chr12:122319572..122322353-chr12:122324355..122326595,2	MCF-7	breast:
5	chr12:122233107..122235013-chr12:122321542..122323051,2	MCF-7	breast:
6	chr12:122233528..122236149-chr12:122319048..122321732,2	K562	blood:
7	chr12:122238851..122242892-chr12:122319516..122321765,3	MCF-7	breast:
8	chr12:122320221..122322912-chr12:122324691..122327698,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000110801	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1168658	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1168661	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1169081	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs1169084	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1169091	0.86[ASW][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs12578258	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs12579730	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs14259	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1720066	0.84[EUR][1000 genomes]
rs1720068	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2272133	0.82[GIH][hapmap]
rs2272135	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2309275	0.95[CEU][hapmap]
rs2442439	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688409	0.90[EUR][1000 genomes]
rs34506529	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34930953	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3825172	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4069666	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760108	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs482421	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs483416	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs508395	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55826938	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56177852	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58379261	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59517025	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71456716	0.94[AFR][1000 genomes]
rs71456717	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7313748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap]
rs830121	0.86[ASW][hapmap];0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs876934	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7309105	WDR66	cis	cerebellum	SCAN
rs7309105	SUDS3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122312000-122322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:122320000-122321800	Enhancers	Liver	Liver
3	chr12:122320400-122322000	Enhancers	K562	blood
4	chr12:122321000-122321800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:122321000-122321800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:122321000-122321800	Enhancers	Hela-S3	cervix
7	chr12:122321000-122322000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:122321200-122321800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:122321200-122321800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:122321200-122322000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:122321400-122321800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:122321400-122321800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr12:122321400-122322000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:122321400-122323000	Enhancers	HepG2	liver
15	chr12:122321400-122325800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:122321400-122326000	Weak transcription	Right Atrium	heart
17	chr12:122321400-122326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:122321400-122326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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