Variant report

Variant	rs7513520
Chromosome Location	chr1:63288932-63288933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10493327	0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10749735	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10889385	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11208032	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11208035	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11208036	0.91[EUR][1000 genomes]
rs11208037	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11208038	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11208040	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11208043	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11208045	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11208046	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11208049	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11208050	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11208051	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11208052	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11208056	0.93[EUR][1000 genomes]
rs11579171	0.86[EUR][1000 genomes]
rs11579518	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11580642	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11584363	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11587081	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11803404	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11804568	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807368	0.81[EUR][1000 genomes]
rs12120847	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12128286	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12129919	0.90[EUR][1000 genomes]
rs12134455	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12567999	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12725996	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12728111	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12742537	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12743698	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12748640	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12749904	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12750156	0.85[EUR][1000 genomes]
rs12752360	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12756081	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1333730	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1333736	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1360678	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1537496	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17097064	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1931079	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1981067	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2366820	0.96[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2366821	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2886771	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3211074	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3737892	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3737893	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4396149	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4448545	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587990	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587991	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587992	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587993	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587994	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587996	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587997	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6587998	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6656119	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6657235	0.90[EUR][1000 genomes]
rs6657707	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6660873	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6665932	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6670072	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6670694	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6676637	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6676821	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6677051	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682286	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6683732	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6685784	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6686232	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6693530	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6695607	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7512374	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7512480	0.81[GIH][hapmap]
rs7512529	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7515960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7519205	0.96[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7521483	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7524508	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7526246	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7527423	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7527905	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7540205	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7553110	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7555606	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs998096	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830015	chr1:63261143-63455296	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7513520	ATG4C	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63250800-63319000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:63251000-63296000	Weak transcription	Fetal Thymus	thymus
3	chr1:63251000-63317800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:63251000-63327400	Weak transcription	Fetal Stomach	stomach
5	chr1:63251200-63327400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:63257400-63293400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:63261600-63326400	Weak transcription	Placenta	Placenta
8	chr1:63262800-63293000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:63267200-63327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:63267200-63327400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:63268400-63297000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:63268600-63319600	Weak transcription	Liver	Liver
13	chr1:63268800-63317600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:63269200-63317400	Weak transcription	Dnd41	blood
15	chr1:63269600-63309600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:63270400-63331400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:63271400-63324400	Weak transcription	Pancreas	Pancrea
18	chr1:63271600-63326800	Weak transcription	Aorta	Aorta
19	chr1:63271600-63327400	Weak transcription	Thymus	Thymus
20	chr1:63271800-63324000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:63273000-63311600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:63273200-63291000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:63273200-63299000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:63273200-63306400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:63273200-63313800	Weak transcription	HSMM	muscle
26	chr1:63273600-63289000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:63273600-63322400	Weak transcription	Ovary	ovary
28	chr1:63273800-63329000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:63274000-63292600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:63274600-63294200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:63275000-63321400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:63275400-63293000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:63275800-63289200	Weak transcription	NH-A	brain
34	chr1:63276000-63322800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:63276400-63295200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:63276400-63311600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:63276400-63312200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:63276400-63322600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:63276600-63299800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:63276600-63323200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:63276600-63324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:63276800-63322000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:63276800-63331400	Weak transcription	Fetal Lung	lung
44	chr1:63277000-63294600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:63277600-63293000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:63277600-63298000	Weak transcription	Adipose Nuclei	Adipose
47	chr1:63277600-63320600	Weak transcription	Right Ventricle	heart
48	chr1:63277600-63327600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:63277800-63299400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:63278000-63299800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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