Variant report

Variant	rs7562069
Chromosome Location	chr2:48597559-48597560
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:

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.94[ASN][1000 genomes]
rs10174717	0.89[AMR][1000 genomes]
rs10186237	0.84[CEU][hapmap]
rs10199431	0.85[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes]
rs10208124	0.84[AMR][1000 genomes]
rs10208627	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10454133	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs10454134	0.83[JPT][hapmap]
rs10495951	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10495952	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11676168	0.85[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes]
rs11679523	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11680916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11682044	0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs11682633	0.92[ASN][1000 genomes]
rs11682931	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11683099	0.95[ASN][1000 genomes]
rs11683639	0.87[JPT][hapmap]
rs11685861	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11686007	0.86[ASN][1000 genomes]
rs11687708	0.81[ASN][1000 genomes]
rs11688481	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11689622	0.87[JPT][hapmap]
rs11689645	0.94[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12052754	0.97[ASN][1000 genomes]
rs12105983	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12328506	0.94[ASN][1000 genomes]
rs13383364	0.81[AMR][1000 genomes]
rs13385535	0.89[AMR][1000 genomes]
rs13387171	0.84[AMR][1000 genomes]
rs13388291	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs13392004	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13398791	0.94[ASN][1000 genomes]
rs13401749	0.87[JPT][hapmap]
rs13432998	0.87[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes]
rs17037289	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17037298	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17855177	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28841370	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4411759	0.85[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.94[ASN][1000 genomes]
rs4547573	0.81[CEU][hapmap]
rs4606978	0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap]
rs55660911	0.99[ASN][1000 genomes]
rs55744465	0.92[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.81[ASN][1000 genomes]
rs56156294	0.92[ASN][1000 genomes]
rs56163539	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56365822	0.83[ASN][1000 genomes]
rs56391806	0.92[ASN][1000 genomes]
rs57131168	0.85[ASN][1000 genomes]
rs57537506	0.96[ASN][1000 genomes]
rs57668696	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57893565	0.97[ASN][1000 genomes]
rs58012056	0.98[ASN][1000 genomes]
rs58978223	0.82[ASN][1000 genomes]
rs59045263	0.86[ASN][1000 genomes]
rs59697023	0.84[ASN][1000 genomes]
rs59761994	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60042255	0.83[ASN][1000 genomes]
rs60815228	0.83[ASN][1000 genomes]
rs60825643	0.94[ASN][1000 genomes]
rs61303367	0.83[ASN][1000 genomes]
rs62136987	0.89[AMR][1000 genomes]
rs62137002	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62137003	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62137015	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62137018	0.81[ASN][1000 genomes]
rs62137019	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62137021	0.83[ASN][1000 genomes]
rs62137041	0.81[AMR][1000 genomes]
rs6545027	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs6545030	0.89[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545034	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545035	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545036	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545039	0.85[EUR][1000 genomes]
rs66705539	0.85[ASN][1000 genomes]
rs6705802	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6712029	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6718068	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs6722246	1.00[ASN][1000 genomes]
rs6735288	0.86[ASN][1000 genomes]
rs6743757	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6745580	0.96[ASN][1000 genomes]
rs6747441	0.80[ASN][1000 genomes]
rs6749773	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756596	0.97[ASN][1000 genomes]
rs6757206	0.89[AMR][1000 genomes]
rs72818488	0.84[ASN][1000 genomes]
rs72818491	0.82[ASN][1000 genomes]
rs72818494	0.83[ASN][1000 genomes]
rs72818502	0.88[ASN][1000 genomes]
rs72820403	0.92[ASN][1000 genomes]
rs72820404	0.95[ASN][1000 genomes]
rs72820405	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72820409	0.94[ASN][1000 genomes]
rs72820411	0.94[ASN][1000 genomes]
rs72820415	0.94[ASN][1000 genomes]
rs72820416	0.94[ASN][1000 genomes]
rs72820418	0.94[ASN][1000 genomes]
rs72820420	0.96[ASN][1000 genomes]
rs72820422	0.96[ASN][1000 genomes]
rs72820423	0.98[ASN][1000 genomes]
rs72820424	0.95[ASN][1000 genomes]
rs72820427	0.96[ASN][1000 genomes]
rs72820433	0.96[ASN][1000 genomes]
rs72820436	0.99[ASN][1000 genomes]
rs72820437	1.00[ASN][1000 genomes]
rs72820439	1.00[ASN][1000 genomes]
rs72820441	0.97[ASN][1000 genomes]
rs72820445	1.00[ASN][1000 genomes]
rs72820454	0.83[ASN][1000 genomes]
rs7559431	0.92[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7566239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7568574	0.85[ASN][1000 genomes]
rs7573316	1.00[ASN][1000 genomes]
rs7576964	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs7577237	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7579932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600794	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7606104	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9309152	0.81[AMR][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
rs7562069	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	chr2:48585600-48598000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:48586000-48602000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:48587000-48598400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:48588000-48602000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:48588200-48597800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:48589400-48607400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:48589600-48598600	Strong transcription	Primary B cells from cord blood	blood
35	chr2:48589800-48597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:48589800-48602000	Weak transcription	Brain Anterior Caudate	brain
37	chr2:48590000-48602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:48590000-48602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:48590000-48607400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:48590200-48600800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:48590200-48601800	Weak transcription	Brain Substantia Nigra	brain
42	chr2:48590200-48601800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:48590200-48602000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:48590800-48601200	Weak transcription	HMEC	breast
45	chr2:48591000-48600000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:48591000-48601000	Weak transcription	Brain Hippocampus Middle	brain
47	chr2:48591200-48602000	Weak transcription	Thymus	Thymus
48	chr2:48591600-48601200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:48591600-48602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:48591600-48605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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