Variant report

Variant	rs1217418
Chromosome Location	chr1:114401231-114401232
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	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:
2	chr1:114399687..114402179-chr1:114447630..114449535,2	K562	blood:

Variant related genes	Relation type
ENSG00000118655	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000231128	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10858016	0.83[ASN][1000 genomes]
rs11102678	0.81[ASW][hapmap];0.90[LWK][hapmap]
rs1111695	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs1217375	0.81[ASW][hapmap];0.97[LWK][hapmap];0.86[YRI][hapmap]
rs1217378	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217379	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217385	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217404	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217405	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217406	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217408	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1217409	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217411	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217419	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230682	0.94[ASN][1000 genomes]
rs1230686	0.94[ASN][1000 genomes]
rs1235005	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1310182	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539437	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935836	0.82[YRI][hapmap]
rs1970559	0.97[LWK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2040041	0.91[LWK][hapmap]
rs2185971	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2273758	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs2476599	0.81[ASW][hapmap];0.97[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2476600	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476602	0.81[ASW][hapmap];0.97[LWK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2476604	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488458	0.80[ASW][hapmap]
rs2797414	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs2797416	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789597	0.82[LWK][hapmap]
rs3789598	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789600	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4991898	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537798	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665194	0.81[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672018	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs7555634	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556622	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats 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	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1217418	MAGI3	cis	cerebellum	SCAN
rs1217418	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:114378000-114402600	Weak transcription	Colonic Mucosa	Colon
3	chr1:114391200-114401800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:114396600-114401600	Strong transcription	Thymus	Thymus
6	chr1:114396800-114401600	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:114396800-114401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:114396800-114402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:114396800-114402000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:114396800-114402200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:114397000-114401600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:114397000-114401800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:114397000-114401800	Strong transcription	Fetal Thymus	thymus
14	chr1:114397000-114402400	Strong transcription	Dnd41	blood
15	chr1:114397400-114402000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:114397600-114402600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:114397800-114401800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:114397800-114402000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:114397800-114409800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:114399200-114402600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:114399200-114402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:114399400-114401800	Enhancers	Primary B cells from cord blood	blood
23	chr1:114399400-114401800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:114399400-114401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:114399400-114402000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:114399400-114402000	Weak transcription	NHEK	skin
27	chr1:114399400-114402200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:114399400-114402200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:114399400-114402600	Weak transcription	HSMM	muscle
30	chr1:114399400-114403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:114399400-114403200	Weak transcription	HSMMtube	muscle
32	chr1:114399600-114401800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:114399600-114401800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:114399800-114401800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:114399800-114401800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:114400000-114401800	Enhancers	Primary B cells from peripheral blood	blood
37	chr1:114400000-114402000	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:114400000-114402000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:114400000-114402200	Flanking Active TSS	GM12878-XiMat	blood
40	chr1:114400200-114401800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:114400200-114402000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:114400200-114402000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:114400200-114405600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:114400400-114401400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:114400800-114401800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:114401000-114401400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:114401000-114401800	Enhancers	K562	blood
48	chr1:114401200-114401400	Strong transcription	Small Intestine	intestine

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