Variant report

Variant	rs2480772
Chromosome Location	chr1:10609460-10609461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10589627..10591241-chr1:10607715..10610040,2	K562	blood:
2	chr1:10599611..10603439-chr1:10608820..10611916,3	K562	blood:
3	chr1:10608473..10610056-chr1:10690153..10691726,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10157111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10157119	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746495	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779739	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779743	0.97[ASN][1000 genomes]
rs10779744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10864461	0.86[EUR][1000 genomes]
rs10864463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864465	0.85[EUR][1000 genomes]
rs11121584	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11121585	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121588	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121593	0.98[ASN][1000 genomes]
rs11121594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11121596	0.86[EUR][1000 genomes]
rs11121597	0.86[EUR][1000 genomes]
rs12033275	1.00[CEU][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs12128630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129678	0.86[EUR][1000 genomes]
rs12133103	0.96[ASN][1000 genomes]
rs12565494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12750901	0.92[ASN][1000 genomes]
rs12753364	0.98[ASN][1000 genomes]
rs17035156	0.95[GIH][hapmap]
rs2039175	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039176	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2086650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2183377	0.89[EUR][1000 genomes]
rs2480771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480775	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480780	0.84[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs2480781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2480786	0.90[GIH][hapmap]
rs2480787	0.83[EUR][1000 genomes]
rs2480789	1.00[GIH][hapmap]
rs2483678	0.95[GIH][hapmap]
rs2506878	1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2506887	0.95[GIH][hapmap]
rs2506888	0.84[EUR][1000 genomes]
rs2506897	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2506898	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2506900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2988398	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34230252	0.98[ASN][1000 genomes]
rs35409029	1.00[ASN][1000 genomes]
rs35612158	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240914	0.84[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4240915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617401	0.89[ASN][1000 genomes]
rs4845936	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4846237	0.96[ASN][1000 genomes]
rs58788814	0.86[EUR][1000 genomes]
rs61777207	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61777208	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540937	0.98[ASN][1000 genomes]
rs6540938	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs6658073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661757	0.98[ASN][1000 genomes]
rs6663688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6663898	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6664134	0.98[ASN][1000 genomes]
rs6681221	0.86[EUR][1000 genomes]
rs6687502	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs6687622	0.98[ASN][1000 genomes]
rs6700023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700886	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs710130	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs72641424	0.85[EUR][1000 genomes]
rs72641427	0.82[EUR][1000 genomes]
rs747124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7512467	1.00[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7519424	1.00[ASN][1000 genomes]
rs7524790	0.92[ASN][1000 genomes]
rs7534954	0.95[ASN][1000 genomes]
rs7545184	0.88[EUR][1000 genomes]
rs944191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661121	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2480772	VAMP3	cis	parietal	SCAN
rs2480772	Hs.211939	cis	multi-tissue	Pritchard
rs2480772	PEX14	cis	Lymphoblastoid	GTEx
rs2480772	PEX14	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
3	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
4	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:10598600-10621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:10599800-10610000	Weak transcription	Stomach Mucosa	stomach
9	chr1:10600000-10615600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:10600000-10615800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:10600000-10619600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:10600200-10614800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:10600200-10615800	Weak transcription	HSMM	muscle
14	chr1:10601000-10613000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:10601200-10613400	Weak transcription	Osteobl	bone
16	chr1:10601200-10619600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:10601400-10610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:10601400-10611000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:10601400-10611000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:10601400-10615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:10601800-10610000	Weak transcription	Fetal Lung	lung
22	chr1:10601800-10610000	Weak transcription	A549	lung
23	chr1:10601800-10610000	Weak transcription	HUVEC	blood vessel
24	chr1:10601800-10613200	Weak transcription	K562	blood
25	chr1:10601800-10613400	Weak transcription	Right Ventricle	heart
26	chr1:10602000-10609800	Weak transcription	Colonic Mucosa	Colon
27	chr1:10602000-10610000	Weak transcription	Gastric	stomach
28	chr1:10602000-10610200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:10602000-10610200	Weak transcription	HepG2	liver
30	chr1:10602000-10610600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:10602000-10610800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:10602000-10610800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:10602000-10611400	Weak transcription	Ovary	ovary
34	chr1:10602000-10612800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:10602000-10612800	Weak transcription	Fetal Thymus	thymus
36	chr1:10602000-10613000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:10602000-10613200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:10602000-10615600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:10602000-10615600	Weak transcription	HMEC	breast
40	chr1:10602000-10616200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:10602000-10619400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:10602000-10639600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:10602200-10609600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:10602200-10615600	Weak transcription	Placenta	Placenta
45	chr1:10602200-10615600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:10602400-10610400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:10602400-10613000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:10602400-10613200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:10602400-10613200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:10602400-10613600	Weak transcription	Primary B cells from peripheral blood	blood

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