Variant report

Variant	rs925095
Chromosome Location	chr17:17344653-17344654
allele	C/T
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	chr17:17329242..17331427-chr17:17343296..17345855,2	MCF-7	breast:
2	chr17:17341170..17345071-chr17:17347034..17351413,6	MCF-7	breast:
3	chr17:17344282..17356772-chr17:17394630..17405312,31	MCF-7	breast:
4	chr17:17261706..17263855-chr17:17343198..17345189,2	MCF-7	breast:
5	chr17:17290703..17292981-chr17:17343527..17346178,2	MCF-7	breast:
6	chr17:17342531..17346072-chr17:17347773..17351460,6	MCF-7	breast:
7	chr17:17335771..17338449-chr17:17342663..17345052,2	MCF-7	breast:
8	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
9	chr17:17344606..17346836-chr17:17348575..17350374,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1123297	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650117	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654572	0.99[ASN][1000 genomes]
rs12449517	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202703	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28489441	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502596	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7212942	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7216896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501994	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075087	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9899529	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058849	chr17:17308009-17348548	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1058804	chr17:17308984-17348548	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv574523	chr17:17310886-17347995	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1056137	chr17:17311017-17348939	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv543235	chr17:17311017-17348939	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv515800	chr17:17322196-17344653	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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 target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs925095	ATPAF2	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17330200-17350000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:17335400-17348800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:17339200-17346800	Weak transcription	Thymus	Thymus
4	chr17:17339600-17347000	Weak transcription	HUVEC	blood vessel
5	chr17:17341400-17346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:17343000-17344800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:17343000-17344800	Enhancers	Hela-S3	cervix
8	chr17:17343000-17345000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr17:17343200-17344800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr17:17343200-17344800	Enhancers	K562	blood
11	chr17:17343400-17344800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr17:17343400-17344800	Enhancers	Brain Anterior Caudate	brain
13	chr17:17343400-17344800	Enhancers	Brain Germinal Matrix	brain
14	chr17:17343400-17344800	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:17343400-17344800	Enhancers	Fetal Muscle Leg	muscle
16	chr17:17343400-17344800	Enhancers	Pancreas	Pancrea
17	chr17:17343400-17344800	Enhancers	NHDF-Ad	bronchial
18	chr17:17343400-17345000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr17:17343400-17345000	Enhancers	Fetal Thymus	thymus
20	chr17:17343600-17344800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:17343600-17344800	Enhancers	Brain Substantia Nigra	brain
22	chr17:17343600-17344800	Enhancers	Fetal Brain Female	brain
23	chr17:17343600-17344800	Enhancers	Right Ventricle	heart
24	chr17:17343800-17344800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:17343800-17344800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr17:17344000-17348400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:17344000-17348600	Weak transcription	Gastric	stomach
28	chr17:17344000-17348800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr17:17344000-17348800	Weak transcription	Fetal Heart	heart
30	chr17:17344000-17349000	Weak transcription	Right Atrium	heart
31	chr17:17344000-17350000	Weak transcription	Dnd41	blood
32	chr17:17344200-17344800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:17344200-17344800	Enhancers	A549	lung
34	chr17:17344200-17345000	Enhancers	HepG2	liver
35	chr17:17344200-17346600	Weak transcription	Liver	Liver
36	chr17:17344200-17348400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:17344200-17348600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr17:17344400-17344800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
39	chr17:17344400-17344800	Enhancers	Left Ventricle	heart
40	chr17:17344600-17344800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr17:17344600-17344800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:17344600-17345000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:17344600-17346200	Weak transcription	Fetal Brain Male	brain
44	chr17:17344600-17347000	Weak transcription	Spleen	Spleen
45	chr17:17344600-17348600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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