Variant report

Variant	rs17154040
Chromosome Location	chr7:107005246-107005247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1015411	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs10224503	0.81[AMR][1000 genomes]
rs10234355	0.94[CHB][hapmap]
rs10264412	0.83[AMR][1000 genomes]
rs10267907	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs11535285	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs12112877	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12667527	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12670688	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs12672451	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12673675	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs13230144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17153981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17154091	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs1858888	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2023685	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2066735	0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2107317	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237659	0.81[ASN][1000 genomes]
rs2237660	0.81[ASN][1000 genomes]
rs2237661	0.95[CEU][hapmap];0.81[ASN][1000 genomes]
rs2237665	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237668	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237671	0.83[AMR][1000 genomes]
rs2237677	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2237678	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes]
rs2253146	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2253269	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2253271	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2283038	0.90[CEU][hapmap]
rs2301801	0.83[ASN][1000 genomes]
rs2395868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395869	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2520241	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520242	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520243	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2520245	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2520249	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2520250	0.84[AMR][1000 genomes]
rs2520256	0.84[AMR][1000 genomes]
rs2520268	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2520269	0.83[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2712195	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2712196	0.83[AMR][1000 genomes]
rs2712201	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2712224	0.84[AMR][1000 genomes]
rs3094383	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs34325395	0.84[AMR][1000 genomes]
rs3801964	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs3801966	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4727678	0.87[AMR][1000 genomes]
rs4727679	0.87[AMR][1000 genomes]
rs4727680	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs4727681	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4730235	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730237	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730238	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730245	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs58391518	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62482493	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62482495	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482499	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62482502	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62482503	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62482507	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62483629	0.82[ASN][1000 genomes]
rs62483633	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483634	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62483641	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6949634	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7777950	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785892	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7788271	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788330	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790080	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803151	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791733	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs982447	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs986994	0.91[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17154040	GPR22	cis	multi-tissue	Pritchard
rs17154040	COG5	cis	parietal	SCAN
rs17154040	C7orf66	cis	cerebellum	SCAN
rs17154040	BCAP29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106984400-107006200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:106986000-107013200	Weak transcription	Small Intestine	intestine
3	chr7:106989200-107018800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:106999600-107007600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:107001000-107012200	Weak transcription	NHDF-Ad	bronchial
6	chr7:107001200-107012400	Weak transcription	Fetal Heart	heart
7	chr7:107001200-107013600	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:107001400-107005800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:107001400-107006000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:107001400-107006200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:107001400-107006200	Weak transcription	HMEC	breast
12	chr7:107001400-107006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:107001400-107012200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:107001400-107012200	Weak transcription	Colonic Mucosa	Colon
15	chr7:107001400-107012600	Weak transcription	NH-A	brain
16	chr7:107001400-107013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:107001400-107013800	Weak transcription	Psoas Muscle	Psoas
18	chr7:107001400-107024600	Weak transcription	Lung	lung
19	chr7:107001400-107026800	Weak transcription	Aorta	Aorta
20	chr7:107001400-107027200	Weak transcription	Right Ventricle	heart
21	chr7:107001400-107031200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:107001400-107037600	Weak transcription	Spleen	Spleen
23	chr7:107001400-107053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:107001600-107006000	Weak transcription	NHEK	skin
25	chr7:107001600-107011200	Weak transcription	GM12878-XiMat	blood
26	chr7:107001600-107012600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:107001600-107013000	Weak transcription	Hela-S3	cervix
28	chr7:107001600-107014000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:107001800-107005400	Weak transcription	HSMM	muscle
30	chr7:107001800-107006200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:107002400-107007400	Weak transcription	Fetal Stomach	stomach
32	chr7:107002400-107013200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:107002400-107014400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:107002400-107024200	Weak transcription	Fetal Intestine Small	intestine
35	chr7:107002600-107012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:107002600-107013200	Weak transcription	Osteobl	bone
37	chr7:107002600-107027000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:107002800-107006000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:107002800-107006200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:107002800-107006200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:107002800-107006200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:107002800-107009000	Weak transcription	Brain Angular Gyrus	brain
43	chr7:107002800-107009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr7:107002800-107011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:107002800-107012600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:107002800-107012600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:107002800-107013000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:107002800-107014000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:107002800-107014600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:107002800-107015600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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