Variant report

Variant	rs7566239
Chromosome Location	chr2:48598882-48598883
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	chr2:48337775..48340265-chr2:48597214..48600170,2	MCF-7	breast:
2	chr2:48598202..48600856-chr2:48603158..48604738,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10186237	0.93[YRI][hapmap]
rs10199431	0.88[JPT][hapmap];0.93[YRI][hapmap]
rs10208627	0.85[ASN][1000 genomes]
rs10454133	0.83[JPT][hapmap]
rs10454134	0.84[JPT][hapmap]
rs10495951	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10495952	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11676168	0.91[JPT][hapmap]
rs11679523	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs11680916	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11682044	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs11682633	0.90[ASN][1000 genomes]
rs11683099	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683639	0.87[JPT][hapmap]
rs11685861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[ASN][1000 genomes]
rs11686007	0.84[ASN][1000 genomes]
rs11688481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11689622	0.87[JPT][hapmap]
rs11689645	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11690690	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11690748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11690845	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12052754	0.95[ASN][1000 genomes]
rs12105983	0.85[ASN][1000 genomes]
rs12328506	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13388291	0.86[JPT][hapmap]
rs13398791	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13401749	0.87[JPT][hapmap]
rs13432998	0.87[JPT][hapmap]
rs17037289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17037298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17855177	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4411759	0.87[JPT][hapmap]
rs4438532	0.84[JPT][hapmap]
rs4547570	0.93[ASN][1000 genomes]
rs4547573	0.89[YRI][hapmap]
rs4606978	0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap];0.82[YRI][hapmap]
rs4953572	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs55660911	0.97[ASN][1000 genomes]
rs55744465	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55761545	0.89[ASN][1000 genomes]
rs56156294	0.90[ASN][1000 genomes]
rs56163539	0.86[ASN][1000 genomes]
rs56365822	0.82[ASN][1000 genomes]
rs56391806	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57131168	0.84[ASN][1000 genomes]
rs57537506	0.94[ASN][1000 genomes]
rs57893565	0.96[ASN][1000 genomes]
rs58012056	0.96[ASN][1000 genomes]
rs58978223	0.81[ASN][1000 genomes]
rs59045263	0.85[ASN][1000 genomes]
rs59697023	0.82[ASN][1000 genomes]
rs60042255	0.82[ASN][1000 genomes]
rs60815228	0.81[ASN][1000 genomes]
rs60825643	0.92[ASN][1000 genomes]
rs61303367	0.82[ASN][1000 genomes]
rs62137002	0.86[AFR][1000 genomes]
rs62137015	0.98[ASN][1000 genomes]
rs62137019	0.83[ASN][1000 genomes]
rs62137021	0.82[ASN][1000 genomes]
rs6545026	0.96[YRI][hapmap]
rs6545027	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs6545030	0.92[JPT][hapmap];0.93[YRI][hapmap]
rs6545036	0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs66705539	0.84[ASN][1000 genomes]
rs6705802	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712029	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs6718068	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6722246	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735288	0.84[ASN][1000 genomes]
rs6743757	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6745580	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749773	0.82[ASN][1000 genomes]
rs6756596	0.96[ASN][1000 genomes]
rs72818488	0.83[ASN][1000 genomes]
rs72818491	0.81[ASN][1000 genomes]
rs72818494	0.82[ASN][1000 genomes]
rs72818502	0.87[ASN][1000 genomes]
rs72820403	0.91[ASN][1000 genomes]
rs72820404	0.94[ASN][1000 genomes]
rs72820409	0.93[ASN][1000 genomes]
rs72820411	0.93[ASN][1000 genomes]
rs72820415	0.93[ASN][1000 genomes]
rs72820416	0.93[ASN][1000 genomes]
rs72820418	0.93[ASN][1000 genomes]
rs72820420	0.94[ASN][1000 genomes]
rs72820422	0.95[ASN][1000 genomes]
rs72820423	0.96[ASN][1000 genomes]
rs72820424	0.94[ASN][1000 genomes]
rs72820427	0.95[ASN][1000 genomes]
rs72820433	0.94[ASN][1000 genomes]
rs72820436	0.97[ASN][1000 genomes]
rs72820437	0.99[ASN][1000 genomes]
rs72820439	0.99[ASN][1000 genomes]
rs72820441	0.95[ASN][1000 genomes]
rs72820445	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820454	0.82[ASN][1000 genomes]
rs7559431	0.91[ASN][1000 genomes]
rs7562069	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7562816	0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7568574	0.83[ASN][1000 genomes]
rs7573316	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7576964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7577237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579932	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7600794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[ASN][1000 genomes]
rs7606104	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7566239	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:121 , 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	chr2:48573600-48604000	Weak transcription	Ovary	ovary
3	chr2:48574200-48602000	Weak transcription	Gastric	stomach
4	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
5	chr2:48576200-48602000	Weak transcription	Lung	lung
6	chr2:48576600-48602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:48577800-48602000	Weak transcription	Fetal Kidney	kidney
8	chr2:48577800-48603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:48578600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:48580600-48601800	Weak transcription	Hela-S3	cervix
11	chr2:48580800-48599800	Weak transcription	NHEK	skin
12	chr2:48580800-48602000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:48580800-48602000	Weak transcription	Osteobl	bone
14	chr2:48580800-48604000	Weak transcription	Aorta	Aorta
15	chr2:48581400-48600800	Weak transcription	Spleen	Spleen
16	chr2:48581400-48601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:48581400-48602000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:48581400-48602000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:48581400-48608000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:48581800-48602000	Weak transcription	Pancreas	Pancrea
21	chr2:48581800-48602000	Weak transcription	Right Ventricle	heart
22	chr2:48581800-48604800	Weak transcription	Psoas Muscle	Psoas
23	chr2:48582000-48600800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:48584400-48602000	Weak transcription	Brain Angular Gyrus	brain
25	chr2:48584600-48601000	Weak transcription	Fetal Lung	lung
26	chr2:48584800-48604400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:48585000-48600600	Weak transcription	HUVEC	blood vessel
28	chr2:48586000-48602000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:48588000-48602000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:48589400-48607400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:48589800-48602000	Weak transcription	Brain Anterior Caudate	brain
32	chr2:48590000-48602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:48590000-48602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:48590000-48607400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:48590200-48600800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:48590200-48601800	Weak transcription	Brain Substantia Nigra	brain
37	chr2:48590200-48601800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:48590200-48602000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:48590800-48601200	Weak transcription	HMEC	breast
40	chr2:48591000-48600000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:48591000-48601000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:48591200-48602000	Weak transcription	Thymus	Thymus
43	chr2:48591600-48601200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:48591600-48602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:48591600-48605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:48592200-48600800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:48592800-48602000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:48592800-48602000	Weak transcription	NHLF	lung
49	chr2:48592800-48605400	Strong transcription	HepG2	liver
50	chr2:48593000-48599800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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