Variant report

Variant	rs9909726
Chromosome Location	chr17:67249922-67249923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67249068..67251344-chr5:90676320..90677864,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11544715	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11871086	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs13313572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345462	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1420905	1.00[EUR][1000 genomes]
rs1468512	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs16973904	1.00[JPT][hapmap]
rs17686569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17759819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1992741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs477045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536009	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57758461	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62080888	0.97[EUR][1000 genomes]
rs62080893	0.84[EUR][1000 genomes]
rs6501290	1.00[JPT][hapmap]
rs67740186	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8064431	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9907148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997639	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv1055156	chr17:67239695-67272311	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a
5	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9909726	ABCA5	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67230600-67259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr17:67230800-67253400	Weak transcription	Fetal Muscle Leg	muscle
3	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
4	chr17:67231800-67252600	Weak transcription	Fetal Thymus	thymus
5	chr17:67231800-67254400	Weak transcription	Lung	lung
6	chr17:67234800-67250600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:67236000-67283000	Weak transcription	Ovary	ovary
9	chr17:67236400-67252400	Weak transcription	Fetal Lung	lung
10	chr17:67236400-67278000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:67236600-67251600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr17:67236800-67280800	Weak transcription	Brain Angular Gyrus	brain
13	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
14	chr17:67238800-67278000	Weak transcription	Thymus	Thymus
15	chr17:67239200-67262400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:67239400-67252400	Weak transcription	HMEC	breast
17	chr17:67239600-67251000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
19	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:67242000-67260600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:67242000-67265000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:67242200-67250400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:67242200-67265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:67242200-67265000	Weak transcription	NHEK	skin
25	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr17:67242800-67256400	Weak transcription	Small Intestine	intestine
27	chr17:67243000-67264800	Weak transcription	NHDF-Ad	bronchial
28	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr17:67244000-67262400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
31	chr17:67244200-67254200	Weak transcription	Colonic Mucosa	Colon
32	chr17:67244400-67251400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:67244600-67252000	Strong transcription	Liver	Liver
34	chr17:67244800-67251600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:67244800-67253800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:67245200-67252200	Weak transcription	Fetal Brain Male	brain
37	chr17:67245600-67261600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:67245800-67255200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:67245800-67278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr17:67246800-67251400	Strong transcription	Adipose Nuclei	Adipose
41	chr17:67246800-67255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr17:67247000-67251400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr17:67247400-67250200	Weak transcription	NH-A	brain
44	chr17:67247400-67250400	Weak transcription	Osteobl	bone
45	chr17:67247400-67250600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr17:67247400-67251000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:67247400-67251600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr17:67247600-67251400	Strong transcription	Fetal Intestine Large	intestine
49	chr17:67247600-67253000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr17:67247800-67251600	Strong transcription	Skeletal Muscle Male	skeletal muscle

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