Variant report

Variant	rs11650955
Chromosome Location	chr17:67235705-67235706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67231929..67233589-chr17:67235089..67237342,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1011549	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10445224	0.89[ASN][1000 genomes]
rs10491177	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10512526	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10512527	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11077445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs112914	0.95[JPT][hapmap]
rs11649744	0.83[ASN][1000 genomes]
rs11650658	0.81[ASN][1000 genomes]
rs11651815	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11651872	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11652207	0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11654323	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11656389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11656456	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs11869324	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11871771	0.83[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12449649	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12450167	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12450402	0.83[ASN][1000 genomes]
rs12450522	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12450743	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12452340	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12937191	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12937947	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12938039	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs12938064	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12938097	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12940364	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12941297	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12942763	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12942867	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12943504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12944980	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12945481	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12945908	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12946566	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12946776	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12949267	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12952942	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1550828	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1558168	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs15886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1990248	0.88[ASN][1000 genomes]
rs2364996	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2441358	0.81[ASN][1000 genomes]
rs34334829	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34609440	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34985085	0.83[ASN][1000 genomes]
rs4310935	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4310936	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs471193	0.95[JPT][hapmap]
rs475283	0.90[JPT][hapmap]
rs476677	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs481876	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs486840	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs494946	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs531586	0.88[JPT][hapmap]
rs534645	0.95[JPT][hapmap]
rs544940	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs557491	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs55773491	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs568536	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs57949169	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58634970	0.83[ASN][1000 genomes]
rs6501313	0.95[JPT][hapmap]
rs7213377	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7223895	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7225762	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs817121	0.95[JPT][hapmap]
rs817126	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs817127	0.82[ASN][1000 genomes]
rs9646388	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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
rs11650955	ABCA5	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
2	chr17:67207600-67247800	Weak transcription	Left Ventricle	heart
3	chr17:67215600-67239200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:67215600-67249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:67224600-67248600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr17:67226800-67236400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr17:67230200-67235800	Weak transcription	Fetal Lung	lung
8	chr17:67230600-67241400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:67230600-67259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:67230800-67253400	Weak transcription	Fetal Muscle Leg	muscle
11	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
12	chr17:67231600-67237000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr17:67231600-67246600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:67231800-67235800	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:67231800-67236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr17:67231800-67236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:67231800-67236800	Weak transcription	Fetal Intestine Large	intestine
18	chr17:67231800-67238600	Weak transcription	Fetal Intestine Small	intestine
19	chr17:67231800-67239000	Weak transcription	GM12878-XiMat	blood
20	chr17:67231800-67239200	Weak transcription	Liver	Liver
21	chr17:67231800-67247000	Weak transcription	Primary T cells from cord blood	blood
22	chr17:67231800-67247000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr17:67231800-67247000	Weak transcription	HUVEC	blood vessel
24	chr17:67231800-67249000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:67231800-67252600	Weak transcription	Fetal Thymus	thymus
26	chr17:67231800-67254400	Weak transcription	Lung	lung
27	chr17:67232000-67236000	Weak transcription	Brain Anterior Caudate	brain
28	chr17:67232200-67236200	Weak transcription	Brain Substantia Nigra	brain
29	chr17:67232600-67249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:67232800-67236200	Weak transcription	Aorta	Aorta
31	chr17:67233000-67238200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:67233400-67235800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:67233600-67245000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr17:67233800-67239800	Weak transcription	Esophagus	oesophagus
35	chr17:67234400-67240200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:67234600-67249200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr17:67234800-67236000	Enhancers	K562	blood
38	chr17:67234800-67236400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:67234800-67250600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr17:67235000-67236000	Enhancers	Ovary	ovary
41	chr17:67235000-67236600	Enhancers	Brain Cingulate Gyrus	brain
42	chr17:67235000-67239400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:67235200-67236800	Enhancers	Brain Angular Gyrus	brain
45	chr17:67235200-67237400	Weak transcription	Adipose Nuclei	Adipose
46	chr17:67235200-67238400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:67235200-67240000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:67235600-67236600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr17:67235600-67239600	Weak transcription	Placenta	Placenta

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