Variant report

Variant	rs6458491
Chromosome Location	chr6:46106992-46106993
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:46106023..46108072-chr6:46120783..46123181,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1011370	0.82[CEU][hapmap]
rs1048076	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048082	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048083	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1076738	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs10807334	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10948280	0.81[AFR][1000 genomes]
rs10948283	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11754760	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11756160	0.84[AFR][1000 genomes]
rs12196107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215921	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526912	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13210366	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14781	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2006030	0.85[AFR][1000 genomes]
rs2143746	0.87[AFR][1000 genomes]
rs2143747	0.93[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179760	0.93[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206965	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2206967	0.84[AFR][1000 genomes]
rs2206968	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2223777	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223778	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235881	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235883	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2894662	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3756801	0.85[AFR][1000 genomes]
rs3756802	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756803	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777634	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806994	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806995	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3905440	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458490	0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902187	0.85[AFR][1000 genomes]
rs6921826	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs6921870	0.85[AFR][1000 genomes]
rs6923745	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926570	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930766	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71566566	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7356841	0.87[AFR][1000 genomes]
rs7356846	0.87[AFR][1000 genomes]
rs7357078	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7451713	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745824	0.84[AFR][1000 genomes]
rs7748442	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7748469	0.83[EUR][1000 genomes]
rs7754582	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7769738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7769902	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7770384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773230	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7775082	0.93[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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180644	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs872859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910179	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349348	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357501	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367233	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9367234	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9367237	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369599	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9381430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9395155	0.84[AFR][1000 genomes]
rs9395156	0.82[GIH][hapmap]
rs9395158	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9395159	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463184	0.85[AFR][1000 genomes]
rs9463185	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472688	0.85[AFR][1000 genomes]
rs9472689	0.84[AFR][1000 genomes]
rs9472690	0.84[AFR][1000 genomes]
rs9472694	0.84[AMR][1000 genomes]
rs9472698	0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472700	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9472704	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9472707	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472708	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472709	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472713	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472715	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs995564	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	nsv1022912	chr6:46093409-46116449	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6458491	ENPP5	cis	parietal	SCAN
rs6458491	MBOAT4	trans	cerebellum	SCAN
rs6458491	ZNF318	cis	parietal	SCAN
rs6458491	ENPP5	cis	Thyroid	GTEx
rs6458491	ENPP5	cis	cerebellum	SCAN
rs6458491	CLIC5	cis	parietal	SCAN
rs6458491	ENPP4	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46098800-46107600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:46098800-46109000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:46098800-46109200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:46098800-46109600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:46098800-46109600	Weak transcription	Fetal Thymus	thymus
6	chr6:46098800-46110200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:46098800-46110200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:46098800-46110400	Weak transcription	Primary B cells from cord blood	blood
9	chr6:46098800-46110400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:46098800-46110600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:46098800-46110600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:46098800-46110600	Weak transcription	Left Ventricle	heart
13	chr6:46098800-46110600	Weak transcription	Dnd41	blood
14	chr6:46098800-46110800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:46098800-46111600	Weak transcription	Right Ventricle	heart
16	chr6:46098800-46112400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:46098800-46112800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:46098800-46112800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:46098800-46112800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:46098800-46113000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:46098800-46117800	Weak transcription	Gastric	stomach
22	chr6:46098800-46129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:46101400-46110600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:46101600-46111800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:46101600-46112000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:46101800-46112000	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:46101800-46113000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:46102000-46110600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:46102200-46110400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:46102200-46113000	Weak transcription	Fetal Intestine Large	intestine
31	chr6:46102400-46107800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:46105000-46114600	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:46105400-46108200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr6:46105400-46110600	Weak transcription	Brain Anterior Caudate	brain
35	chr6:46105400-46110600	Weak transcription	Thymus	Thymus
36	chr6:46105400-46115000	Weak transcription	Aorta	Aorta
37	chr6:46105400-46133800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:46105600-46113200	Weak transcription	Spleen	Spleen
39	chr6:46105600-46128600	Weak transcription	Brain Angular Gyrus	brain
40	chr6:46105600-46137400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:46105800-46112800	Weak transcription	HSMMtube	muscle
42	chr6:46106000-46110400	Weak transcription	Fetal Heart	heart
43	chr6:46106400-46107600	Weak transcription	Brain Substantia Nigra	brain
44	chr6:46106400-46109200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:46106400-46110600	Weak transcription	Pancreas	Pancrea
46	chr6:46106400-46110600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:46106400-46111000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:46106400-46111600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:46106400-46112600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:46106400-46112800	Weak transcription	Brain Hippocampus Middle	brain

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