Variant report

Variant	rs17037289
Chromosome Location	chr2:48587198-48587199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.92[ASN][1000 genomes]
rs10199431	0.87[JPT][hapmap]
rs10208627	0.85[ASN][1000 genomes]
rs10454133	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10454134	0.83[JPT][hapmap]
rs10495951	0.95[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10495952	0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11676168	0.91[JPT][hapmap]
rs11678403	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11679523	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.97[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11680916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11682044	0.83[JPT][hapmap]
rs11682633	0.89[ASN][1000 genomes]
rs11683099	0.94[ASN][1000 genomes]
rs11683639	0.87[JPT][hapmap]
rs11685861	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11686007	0.83[ASN][1000 genomes]
rs11688481	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11689622	0.87[JPT][hapmap]
rs11689645	0.90[ASN][1000 genomes]
rs11690690	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11690748	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11690845	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12052754	0.92[ASN][1000 genomes]
rs12105983	0.85[ASN][1000 genomes]
rs12328506	0.93[ASN][1000 genomes]
rs13388291	0.86[JPT][hapmap]
rs13398791	0.93[ASN][1000 genomes]
rs13401749	0.87[JPT][hapmap]
rs13432998	0.87[JPT][hapmap]
rs17037298	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17855177	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.96[ASN][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4411759	0.87[JPT][hapmap]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.93[ASN][1000 genomes]
rs4606978	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap]
rs55660911	0.97[ASN][1000 genomes]
rs55744465	0.90[ASN][1000 genomes]
rs55761545	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56156294	0.90[ASN][1000 genomes]
rs56163539	0.86[ASN][1000 genomes]
rs56365822	0.82[ASN][1000 genomes]
rs56391806	0.90[ASN][1000 genomes]
rs57131168	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57537506	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57893565	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58012056	0.96[ASN][1000 genomes]
rs58660534	0.84[AFR][1000 genomes]
rs58978223	0.81[ASN][1000 genomes]
rs59045263	0.85[ASN][1000 genomes]
rs59697023	0.81[ASN][1000 genomes]
rs60042255	0.82[ASN][1000 genomes]
rs60825643	0.92[ASN][1000 genomes]
rs61303367	0.82[ASN][1000 genomes]
rs62137007	0.84[AFR][1000 genomes]
rs62137008	0.82[AFR][1000 genomes]
rs62137009	0.84[AFR][1000 genomes]
rs62137015	0.95[ASN][1000 genomes]
rs62137019	0.83[ASN][1000 genomes]
rs62137021	0.82[ASN][1000 genomes]
rs6545027	0.82[JPT][hapmap]
rs6545030	0.91[JPT][hapmap]
rs6545036	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs66705539	0.84[ASN][1000 genomes]
rs6705802	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6712029	0.91[JPT][hapmap]
rs6718068	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6722246	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6735288	0.85[ASN][1000 genomes]
rs6743757	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6745580	0.93[ASN][1000 genomes]
rs6749773	0.82[ASN][1000 genomes]
rs6756596	0.96[ASN][1000 genomes]
rs72818477	0.81[EUR][1000 genomes]
rs72818488	0.82[ASN][1000 genomes]
rs72818494	0.80[ASN][1000 genomes]
rs72818502	0.86[ASN][1000 genomes]
rs72820403	0.90[ASN][1000 genomes]
rs72820404	0.92[ASN][1000 genomes]
rs72820409	0.93[ASN][1000 genomes]
rs72820411	0.92[ASN][1000 genomes]
rs72820415	0.92[ASN][1000 genomes]
rs72820416	0.92[ASN][1000 genomes]
rs72820418	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820420	0.93[ASN][1000 genomes]
rs72820422	0.95[ASN][1000 genomes]
rs72820423	0.96[ASN][1000 genomes]
rs72820424	0.94[ASN][1000 genomes]
rs72820427	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820433	0.99[ASN][1000 genomes]
rs72820436	0.94[ASN][1000 genomes]
rs72820437	0.96[ASN][1000 genomes]
rs72820439	0.96[ASN][1000 genomes]
rs72820441	0.92[ASN][1000 genomes]
rs72820445	0.96[ASN][1000 genomes]
rs72820454	0.82[ASN][1000 genomes]
rs7559431	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562069	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7562816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7566239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7568574	0.83[ASN][1000 genomes]
rs7573316	0.96[ASN][1000 genomes]
rs7576964	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7577237	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs7579932	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7600794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7606104	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17037289	STON1-GTF2A1L	cis	cerebellum	SCAN
rs17037289	GTF2A1L	cis	Esophagus Muscularis	GTEx
rs17037289	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
2	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:48573600-48604000	Weak transcription	Ovary	ovary
4	chr2:48574200-48602000	Weak transcription	Gastric	stomach
5	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
6	chr2:48574800-48589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:48574800-48589600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:48576200-48597000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:48576200-48602000	Weak transcription	Lung	lung
10	chr2:48576400-48590000	Weak transcription	Placenta	Placenta
11	chr2:48576600-48595600	Weak transcription	Fetal Brain Female	brain
12	chr2:48576600-48602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:48577600-48589600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:48577600-48589600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:48577800-48592400	Weak transcription	Right Atrium	heart
16	chr2:48577800-48602000	Weak transcription	Fetal Kidney	kidney
17	chr2:48577800-48603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:48578600-48591000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:48578600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:48578800-48589000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:48578800-48589600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:48579000-48589400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:48579000-48595000	Weak transcription	Esophagus	oesophagus
24	chr2:48579000-48595000	Weak transcription	Fetal Stomach	stomach
25	chr2:48579200-48593000	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:48579200-48595400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:48579400-48589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:48580400-48595200	Weak transcription	HSMMtube	muscle
29	chr2:48580600-48587600	Weak transcription	HSMM	muscle
30	chr2:48580600-48588200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:48580600-48601800	Weak transcription	Hela-S3	cervix
32	chr2:48580800-48589000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:48580800-48591800	Weak transcription	NH-A	brain
34	chr2:48580800-48599800	Weak transcription	NHEK	skin
35	chr2:48580800-48602000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:48580800-48602000	Weak transcription	Osteobl	bone
37	chr2:48580800-48604000	Weak transcription	Aorta	Aorta
38	chr2:48581000-48593400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:48581200-48590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:48581400-48589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:48581400-48589400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:48581400-48589400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:48581400-48589600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:48581400-48589600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:48581400-48589600	Weak transcription	NHLF	lung
46	chr2:48581400-48589800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:48581400-48589800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:48581400-48589800	Weak transcription	HMEC	breast
49	chr2:48581400-48592400	Weak transcription	NHDF-Ad	bronchial
50	chr2:48581400-48600800	Weak transcription	Spleen	Spleen

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