Variant report

Variant	rs1217419
Chromosome Location	chr1:114401904-114401905
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114399687..114402179-chr1:114447630..114449535,2	K562	blood:

Variant related genes	Relation type
ENSG00000118655	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10858016	0.83[ASN][1000 genomes]
rs11102678	0.87[ASW][hapmap];0.85[LWK][hapmap]
rs1111695	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1217375	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1217378	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217379	0.87[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];0.98[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217385	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217404	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217408	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1217409	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217411	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217414	0.83[YRI][hapmap]
rs1217418	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230682	0.94[ASN][1000 genomes]
rs1230686	0.94[ASN][1000 genomes]
rs1235005	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1310182	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13524	0.83[YRI][hapmap]
rs1539437	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935836	0.96[YRI][hapmap]
rs1970559	0.97[LWK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes]
rs2040041	0.91[LWK][hapmap]
rs2185971	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2273758	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs2476599	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2476600	0.87[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];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476602	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2476604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2797414	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.94[ASN][1000 genomes]
rs2797416	0.87[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];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[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[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4991898	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665194	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[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];0.92[MKK][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs7555634	0.87[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];0.98[TSI][hapmap];0.83[YRI][hapmap];0.83[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
rs1217419	PHTF1	cis	cerebellum	SCAN
rs1217419	MAGI3	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	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
4	chr1:114396800-114402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:114396800-114402000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:114396800-114402200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:114397000-114402400	Strong transcription	Dnd41	blood
8	chr1:114397400-114402000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:114397600-114402600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:114397800-114402000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:114397800-114409800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:114399200-114402600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:114399200-114402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:114399400-114402000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:114399400-114402000	Weak transcription	NHEK	skin
16	chr1:114399400-114402200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:114399400-114402200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:114399400-114402600	Weak transcription	HSMM	muscle
19	chr1:114399400-114403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:114399400-114403200	Weak transcription	HSMMtube	muscle
21	chr1:114400000-114402000	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:114400000-114402000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:114400000-114402200	Flanking Active TSS	GM12878-XiMat	blood
24	chr1:114400200-114402000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr1:114400200-114402000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:114400200-114405600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:114401400-114402200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:114401400-114403200	Weak transcription	Small Intestine	intestine
29	chr1:114401600-114402200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:114401600-114403800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:114401600-114406000	Weak transcription	Thymus	Thymus
32	chr1:114401600-114409000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:114401600-114412000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:114401800-114402000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:114401800-114402000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:114401800-114402000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:114401800-114402000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:114401800-114402000	Enhancers	Adipose Nuclei	Adipose
39	chr1:114401800-114402200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:114401800-114402600	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr1:114401800-114402600	Flanking Active TSS	K562	blood
42	chr1:114401800-114403000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:114401800-114403200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:114401800-114403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:114401800-114403400	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:114401800-114404000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:114401800-114404600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:114401800-114410800	Weak transcription	Fetal Thymus	thymus

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