Variant report

Variant	rs7576964
Chromosome Location	chr2:48601448-48601449
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48583541..48585248-chr2:48599640..48601828,2	MCF-7	breast:
2	chr2:48568069..48570400-chr2:48600787..48602390,2	K562	blood:
3	chr2:48592285..48594588-chr2:48601399..48603499,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10153773	0.91[JPT][hapmap]
rs10169629	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10186237	0.82[JPT][hapmap];0.92[YRI][hapmap]
rs10199431	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs10208627	0.86[ASN][1000 genomes]
rs10454133	0.81[CHD][hapmap];0.82[MEX][hapmap]
rs10495951	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10495952	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11676168	0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs11679523	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11680719	0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs11680916	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11682044	0.87[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs11682633	0.92[ASN][1000 genomes]
rs11683099	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11683639	0.82[JPT][hapmap]
rs11685861	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11686007	0.86[ASN][1000 genomes]
rs11687708	0.81[ASN][1000 genomes]
rs11688481	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11689622	0.82[JPT][hapmap]
rs11689645	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12052754	0.97[ASN][1000 genomes]
rs12105983	0.86[ASN][1000 genomes]
rs12328506	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388291	0.81[JPT][hapmap]
rs13398791	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401749	0.82[JPT][hapmap]
rs13432998	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs17037289	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17037298	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17855177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841370	0.82[AFR][1000 genomes]
rs4316980	0.82[JPT][hapmap]
rs4344965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs4411759	0.91[JPT][hapmap];0.82[MEX][hapmap]
rs4547570	0.94[ASN][1000 genomes]
rs4547573	0.88[YRI][hapmap]
rs4606978	0.81[CHD][hapmap]
rs4641990	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs4953572	0.95[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs55660911	0.99[ASN][1000 genomes]
rs55744465	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.81[ASN][1000 genomes]
rs56156294	0.92[ASN][1000 genomes]
rs56163539	0.88[ASN][1000 genomes]
rs56365822	0.83[ASN][1000 genomes]
rs56391806	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57131168	0.85[ASN][1000 genomes]
rs57537506	0.96[ASN][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]
rs60042255	0.83[ASN][1000 genomes]
rs60815228	0.83[ASN][1000 genomes]
rs60825643	0.94[ASN][1000 genomes]
rs61303367	0.83[ASN][1000 genomes]
rs62137003	0.83[AFR][1000 genomes]
rs62137015	0.99[ASN][1000 genomes]
rs62137018	0.81[ASN][1000 genomes]
rs62137019	0.84[ASN][1000 genomes]
rs62137021	0.83[ASN][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545027	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs6545030	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs6545034	0.82[AFR][1000 genomes]
rs6545035	0.82[AFR][1000 genomes]
rs6545036	0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.88[ASN][1000 genomes]
rs66705539	0.85[ASN][1000 genomes]
rs6705802	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712029	0.81[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs6718068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722246	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735288	0.86[ASN][1000 genomes]
rs6743757	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs6745580	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6747441	0.80[ASN][1000 genomes]
rs6749773	0.83[ASN][1000 genomes]
rs6756596	0.97[ASN][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]
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	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820454	0.83[ASN][1000 genomes]
rs7559431	0.92[ASN][1000 genomes]
rs7562069	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7566239	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]
rs7568574	0.85[ASN][1000 genomes]
rs7573316	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577237	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7579932	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7600794	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7606104	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[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
rs7576964	STON1-GTF2A1L	cis	cerebellum	SCAN
rs7576964	PPP1R21	cis	Thyroid	GTEx
rs7576964	FBXO11	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr2:48580800-48602000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:48580800-48602000	Weak transcription	Osteobl	bone
13	chr2:48580800-48604000	Weak transcription	Aorta	Aorta
14	chr2:48581400-48601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:48581400-48602000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:48581400-48602000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:48581400-48608000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:48581800-48602000	Weak transcription	Pancreas	Pancrea
19	chr2:48581800-48602000	Weak transcription	Right Ventricle	heart
20	chr2:48581800-48604800	Weak transcription	Psoas Muscle	Psoas
21	chr2:48584400-48602000	Weak transcription	Brain Angular Gyrus	brain
22	chr2:48584800-48604400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:48586000-48602000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:48588000-48602000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:48589400-48607400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:48589800-48602000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:48590000-48602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:48590000-48602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:48590000-48607400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:48590200-48601800	Weak transcription	Brain Substantia Nigra	brain
31	chr2:48590200-48601800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:48590200-48602000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:48591200-48602000	Weak transcription	Thymus	Thymus
34	chr2:48591600-48602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:48591600-48605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:48592800-48602000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:48592800-48602000	Weak transcription	NHLF	lung
38	chr2:48592800-48605400	Strong transcription	HepG2	liver
39	chr2:48593800-48601800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:48594000-48602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:48594000-48602200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:48594200-48602000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:48594400-48602000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:48595000-48601600	Weak transcription	NH-A	brain
45	chr2:48595000-48602000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:48595200-48609200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:48595800-48602000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:48595800-48602000	Weak transcription	Esophagus	oesophagus
49	chr2:48595800-48602000	Weak transcription	Left Ventricle	heart
50	chr2:48595800-48605000	Weak transcription	Fetal Brain Male	brain

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