Variant report

Variant	rs17099986
Chromosome Location	chr1:77627810-77627811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10493536	0.82[CEU][hapmap]
rs10493602	0.82[CEU][hapmap]
rs1098129	0.90[JPT][hapmap]
rs1103683	0.91[JPT][hapmap]
rs11162319	0.82[CEU][hapmap]
rs1167198	0.82[CEU][hapmap]
rs1167205	0.82[CEU][hapmap]
rs12076479	0.82[CEU][hapmap]
rs12079185	0.82[CEU][hapmap]
rs12079234	0.82[CEU][hapmap]
rs1270993	0.91[JPT][hapmap]
rs1502526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502533	0.91[JPT][hapmap]
rs1502535	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1616272	0.82[CEU][hapmap]
rs1670611	0.82[CEU][hapmap]
rs1670612	0.82[CEU][hapmap]
rs1670617	0.82[CEU][hapmap]
rs17099882	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17099885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17099982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17099983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100185	0.82[CEU][hapmap]
rs17100204	0.82[CEU][hapmap]
rs17100317	0.82[CEU][hapmap]
rs17100319	0.82[CEU][hapmap]
rs17100440	0.82[CEU][hapmap]
rs1721165	0.82[CEU][hapmap]
rs1779178	0.82[CEU][hapmap]
rs1779186	0.90[JPT][hapmap]
rs1974032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054017	0.82[CEU][hapmap]
rs2054018	0.82[CEU][hapmap]
rs2202164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602953	0.82[CEU][hapmap]
rs2653469	0.90[JPT][hapmap]
rs2689674	0.90[JPT][hapmap]
rs2689675	0.90[JPT][hapmap]
rs2689679	0.91[JPT][hapmap]
rs2815313	0.82[CEU][hapmap]
rs3962875	0.82[CEU][hapmap]
rs4033035	0.82[CEU][hapmap]
rs4033036	0.82[CEU][hapmap]
rs4033037	0.82[CEU][hapmap]
rs4033310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55650169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55786631	0.92[ASN][1000 genomes]
rs55957022	0.97[ASN][1000 genomes]
rs55964131	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56079641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56129228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56282465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56938657	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57132154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57715617	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57891552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59013925	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59633783	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60914816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661765	0.82[CEU][hapmap]
rs6665543	0.82[CEU][hapmap]
rs6669724	0.82[CEU][hapmap]
rs6680763	0.82[CEU][hapmap]
rs6683829	0.82[CEU][hapmap]
rs6688757	0.93[ASN][1000 genomes]
rs6703688	0.82[CEU][hapmap]
rs721514	0.82[CEU][hapmap]
rs72681878	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681881	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681891	0.95[ASN][1000 genomes]
rs72681892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72681893	0.95[ASN][1000 genomes]
rs72681895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72681899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72681900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683907	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72683933	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683937	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72683941	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683945	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683947	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524360	0.90[JPT][hapmap]
rs7531431	0.82[CEU][hapmap]
rs7534033	0.82[CEU][hapmap]
rs7537603	0.82[CEU][hapmap]
rs839799	0.91[JPT][hapmap]
rs839820	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs839821	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs839824	0.91[JPT][hapmap]
rs839831	0.91[JPT][hapmap]
rs858447	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17099986	PIGK	Cis_1M	lymphoblastoid	RTeQTL
rs17099986	PIGK	cis	uninvolved skin	skin_eQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77595400-77640400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:77606200-77651600	Weak transcription	Aorta	Aorta
3	chr1:77609800-77628800	Weak transcription	Colonic Mucosa	Colon
4	chr1:77612800-77630200	Weak transcription	Psoas Muscle	Psoas
5	chr1:77614400-77630200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:77614400-77631000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:77614400-77634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:77614400-77634000	Weak transcription	Osteobl	bone
9	chr1:77614400-77635600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:77614400-77635600	Weak transcription	NHDF-Ad	bronchial
11	chr1:77614600-77629600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:77614600-77632000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:77616200-77663200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:77617200-77636000	Weak transcription	HSMM	muscle
15	chr1:77618200-77633000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:77618400-77632200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:77618400-77633200	Weak transcription	Fetal Brain Male	brain
18	chr1:77618600-77630000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:77618600-77630600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:77618600-77633000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:77618600-77634600	Weak transcription	Right Ventricle	heart
22	chr1:77619000-77638000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:77619000-77640200	Weak transcription	A549	lung
24	chr1:77620200-77633200	Weak transcription	Brain Angular Gyrus	brain
25	chr1:77621000-77628200	Weak transcription	Liver	Liver
26	chr1:77621000-77632200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:77621000-77641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:77621800-77634000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:77622600-77633800	Weak transcription	HUVEC	blood vessel
30	chr1:77623200-77630000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:77623200-77631400	Weak transcription	Spleen	Spleen
32	chr1:77623200-77639400	Weak transcription	Fetal Lung	lung
33	chr1:77623400-77641000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:77623800-77628800	Weak transcription	K562	blood
35	chr1:77624000-77629000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:77624000-77629000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:77624000-77630800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:77624200-77630800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:77624600-77629200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:77624800-77629200	Strong transcription	Primary T cells from cord blood	blood
41	chr1:77625000-77630000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:77625000-77634200	Weak transcription	Esophagus	oesophagus
43	chr1:77625200-77631600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:77625400-77628000	Strong transcription	Adipose Nuclei	Adipose
45	chr1:77625400-77630400	Weak transcription	Gastric	stomach
46	chr1:77625600-77628000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:77625600-77628000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:77625600-77629000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:77625600-77630200	Weak transcription	GM12878-XiMat	blood
50	chr1:77625600-77631800	Weak transcription	Fetal Muscle Trunk	muscle

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