Variant report

Variant	rs1123297
Chromosome Location	chr17:17343611-17343612
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17255909..17258113-chr17:17342308..17343826,2	MCF-7	breast:
2	chr17:17329242..17331427-chr17:17343296..17345855,2	MCF-7	breast:
3	chr17:17341170..17345071-chr17:17347034..17351413,6	MCF-7	breast:
4	chr17:17261706..17263855-chr17:17343198..17345189,2	MCF-7	breast:
5	chr17:17291138..17292058-chr17:17343026..17343970,5	MCF-7	breast:
6	chr17:17290703..17292981-chr17:17343527..17346178,2	MCF-7	breast:
7	chr17:17342531..17346072-chr17:17347773..17351460,6	MCF-7	breast:
8	chr17:17336920..17339471-chr17:17342851..17344452,2	MCF-7	breast:
9	chr17:17335771..17338449-chr17:17342663..17345052,2	MCF-7	breast:
10	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
11	chr17:17258968..17259852-chr17:17343043..17343948,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11650117	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654572	0.99[ASN][1000 genomes]
rs1242482	0.95[LWK][hapmap];0.84[YRI][hapmap]
rs12449517	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202703	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28489441	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925141	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502596	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7212942	0.83[AMR][1000 genomes]
rs7216896	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075087	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs925095	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]

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	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	nsv1062207	chr17:17310099-17344599	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv543234	chr17:17310099-17344599	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs1123297	ATPAF2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr17:17338800-17343800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:17339200-17346800	Weak transcription	Thymus	Thymus
5	chr17:17339400-17343800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:17339600-17347000	Weak transcription	HUVEC	blood vessel
7	chr17:17341400-17346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr17:17341600-17344600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:17343000-17343800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr17:17343000-17344800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:17343000-17344800	Enhancers	Hela-S3	cervix
12	chr17:17343000-17345000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr17:17343200-17343800	Enhancers	Primary T cells from cord blood	blood
14	chr17:17343200-17343800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:17343200-17343800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr17:17343200-17344200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr17:17343200-17344800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr17:17343200-17344800	Enhancers	K562	blood
19	chr17:17343400-17343800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:17343400-17343800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr17:17343400-17343800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:17343400-17343800	Enhancers	Placenta	Placenta
23	chr17:17343400-17344000	Enhancers	Fetal Heart	heart
24	chr17:17343400-17344000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:17343400-17344000	Enhancers	Gastric	stomach
26	chr17:17343400-17344000	ZNF genes & repeats	Right Atrium	heart
27	chr17:17343400-17344200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:17343400-17344200	Flanking Active TSS	A549	lung
29	chr17:17343400-17344200	Enhancers	NH-A	brain
30	chr17:17343400-17344600	Enhancers	Spleen	Spleen
31	chr17:17343400-17344800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr17:17343400-17344800	Enhancers	Brain Anterior Caudate	brain
33	chr17:17343400-17344800	Enhancers	Brain Germinal Matrix	brain
34	chr17:17343400-17344800	Enhancers	Fetal Muscle Trunk	muscle
35	chr17:17343400-17344800	Enhancers	Fetal Muscle Leg	muscle
36	chr17:17343400-17344800	Enhancers	Pancreas	Pancrea
37	chr17:17343400-17344800	Enhancers	NHDF-Ad	bronchial
38	chr17:17343400-17345000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr17:17343400-17345000	Enhancers	Fetal Thymus	thymus
40	chr17:17343600-17343800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:17343600-17343800	Enhancers	Lung	lung
42	chr17:17343600-17344000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr17:17343600-17344000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr17:17343600-17344000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr17:17343600-17344000	Enhancers	Dnd41	blood
46	chr17:17343600-17344200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr17:17343600-17344200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:17343600-17344200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:17343600-17344200	Enhancers	Liver	Liver
50	chr17:17343600-17344200	Enhancers	Left Ventricle	heart

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