Variant report

Variant	rs1550828
Chromosome Location	chr17:67282332-67282333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1011549	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10445224	0.93[ASN][1000 genomes]
rs10491177	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10512526	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10512527	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11077445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs112914	0.95[JPT][hapmap]
rs11649744	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11650658	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11650955	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]
rs11651815	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651872	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652207	0.89[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11654323	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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11656456	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11869324	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871771	0.85[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12449649	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450167	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450402	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12450522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12450743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12937191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12937947	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12938039	0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12938064	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938097	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940364	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12941297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12942763	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12942867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12943504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12944980	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12945481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12945908	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12946566	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12946776	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949267	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12952942	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1558168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs15886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1990248	0.82[ASN][1000 genomes]
rs2364996	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2441358	0.88[ASN][1000 genomes]
rs34334829	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34609440	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34985085	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4310935	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4310936	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs471193	0.95[JPT][hapmap]
rs475283	0.90[JPT][hapmap]
rs476677	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs481876	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs486840	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs488714	0.82[ASN][1000 genomes]
rs494946	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs523505	0.84[ASN][1000 genomes]
rs531586	0.88[JPT][hapmap]
rs534645	0.95[JPT][hapmap]
rs544940	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs557491	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs55773491	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568536	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs57949169	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58634970	0.83[EUR][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];0.85[ASN][1000 genomes]
rs7225762	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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	0.87[ASN][1000 genomes]
rs9646388	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	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	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
5	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv1063768	chr17:67268342-67311136	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
9	esv1799828	chr17:67280310-67309039	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1550828	PRKAR1A	cis	cerebellum	SCAN
rs1550828	ABCA5	cis	cerebellum	SCAN
rs1550828	GH2	cis	cerebellum	SCAN
rs1550828	GH2	cis	parietal	SCAN
rs1550828	C17orf58	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:67236000-67283000	Weak transcription	Ovary	ovary
3	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
4	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
5	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
9	chr17:67248000-67284400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr17:67250000-67289200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:67251600-67289200	Weak transcription	Brain Anterior Caudate	brain
12	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:67265000-67289200	Weak transcription	Lung	lung
14	chr17:67265000-67289800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:67266000-67282400	Weak transcription	HMEC	breast
16	chr17:67266200-67290000	Weak transcription	Fetal Heart	heart
17	chr17:67266200-67310400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:67266800-67282400	Weak transcription	NHDF-Ad	bronchial
19	chr17:67267600-67283400	Weak transcription	HUVEC	blood vessel
20	chr17:67268600-67295400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr17:67270200-67307400	Weak transcription	Colonic Mucosa	Colon
22	chr17:67270600-67289600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr17:67271000-67289200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:67271000-67298600	Weak transcription	Fetal Lung	lung
25	chr17:67271400-67296000	Weak transcription	Fetal Kidney	kidney
26	chr17:67272400-67306400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:67272800-67289200	Weak transcription	Pancreas	Pancrea
28	chr17:67274600-67288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:67275800-67289200	Weak transcription	Fetal Muscle Leg	muscle
30	chr17:67276200-67289200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:67276400-67310600	Weak transcription	Brain Substantia Nigra	brain
32	chr17:67276600-67308800	Weak transcription	Aorta	Aorta
33	chr17:67277000-67283000	Weak transcription	Small Intestine	intestine
34	chr17:67277200-67289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:67277600-67283000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:67277600-67285200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr17:67277600-67286000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:67277600-67288600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:67277600-67289000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:67277600-67289200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr17:67277600-67289200	Strong transcription	Liver	Liver
42	chr17:67277600-67293600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:67277800-67284600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr17:67277800-67285000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr17:67277800-67286000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:67277800-67297000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr17:67278000-67286200	Strong transcription	Adipose Nuclei	Adipose
48	chr17:67278000-67292000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:67278200-67284600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr17:67278200-67285000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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