Variant report

Variant	rs997639
Chromosome Location	chr17:67237750-67237751
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	chr17:67237020..67239895-chr17:67240167..67242390,3	MCF-7	breast:
2	chr17:67235995..67239986-chr17:67240583..67244208,4	K562	blood:

Variant related genes	Relation type
ENSG00000154263	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11544715	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];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][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[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345462	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17759819	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992741	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs536009	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs56389663	0.81[AFR][1000 genomes]
rs57758461	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62080888	0.97[EUR][1000 genomes]
rs62080893	0.84[EUR][1000 genomes]
rs6501290	1.00[JPT][hapmap]
rs67740186	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8064431	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9907148	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9907847	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909726	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:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs997639	ABCA5	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67207600-67247800	Weak transcription	Left Ventricle	heart
2	chr17:67215600-67239200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:67215600-67249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:67224600-67248600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr17:67230600-67241400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:67230600-67259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:67230800-67253400	Weak transcription	Fetal Muscle Leg	muscle
8	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
9	chr17:67231600-67246600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:67231800-67238600	Weak transcription	Fetal Intestine Small	intestine
11	chr17:67231800-67239000	Weak transcription	GM12878-XiMat	blood
12	chr17:67231800-67239200	Weak transcription	Liver	Liver
13	chr17:67231800-67247000	Weak transcription	Primary T cells from cord blood	blood
14	chr17:67231800-67247000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:67231800-67247000	Weak transcription	HUVEC	blood vessel
16	chr17:67231800-67249000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:67231800-67252600	Weak transcription	Fetal Thymus	thymus
18	chr17:67231800-67254400	Weak transcription	Lung	lung
19	chr17:67232600-67249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:67233000-67238200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:67233600-67245000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr17:67233800-67239800	Weak transcription	Esophagus	oesophagus
23	chr17:67234400-67240200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:67234600-67249200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:67234800-67250600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr17:67235000-67239400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr17:67235200-67238400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:67235200-67240000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr17:67235600-67239600	Weak transcription	Placenta	Placenta
31	chr17:67236000-67238800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr17:67236000-67283000	Weak transcription	Ovary	ovary
33	chr17:67236400-67252400	Weak transcription	Fetal Lung	lung
34	chr17:67236400-67278000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:67236600-67239000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr17:67236600-67241400	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:67236600-67241800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:67236600-67248600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr17:67236600-67251600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:67236800-67240000	Strong transcription	Fetal Intestine Large	intestine
41	chr17:67236800-67249000	Weak transcription	Brain Anterior Caudate	brain
42	chr17:67236800-67280800	Weak transcription	Brain Angular Gyrus	brain
43	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
44	chr17:67237000-67237800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr17:67237200-67239400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:67237200-67244600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr17:67237200-67246400	Weak transcription	Aorta	Aorta
48	chr17:67237400-67238000	Strong transcription	Adipose Nuclei	Adipose

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