Variant report

Variant	rs1217414
Chromosome Location	chr1:114412667-114412668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114411338..114413654-chr1:114445922..114448240,2	MCF-7	breast:
2	chr1:114353848..114356289-chr1:114410942..114413030,2	K562	blood:
3	chr1:114408080..114410275-chr1:114410974..114412985,2	MCF-7	breast:
4	chr1:114377680..114381184-chr1:114408500..114412874,4	MCF-7	breast:
5	chr1:114410218..114413030-chr1:114439150..114442728,3	K562	blood:
6	chr1:114352486..114355965-chr1:114410764..114413351,3	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11102678	0.81[ASW][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap]
rs12144309	0.86[GIH][hapmap]
rs1217375	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1217382	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs1217385	0.89[LWK][hapmap]
rs1217393	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs1217397	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1217401	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1217403	0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217406	0.82[YRI][hapmap]
rs1217408	0.81[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217417	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1217419	0.83[YRI][hapmap]
rs1217423	0.80[CEU][hapmap]
rs1230681	0.90[JPT][hapmap]
rs1235005	0.94[LWK][hapmap];0.87[YRI][hapmap]
rs13524	1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs1746857	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1746860	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1935836	0.90[JPT][hapmap];0.87[YRI][hapmap]
rs1970559	1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040041	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs2185827	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2476599	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2476602	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789597	0.85[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap]
rs3789598	0.86[ASW][hapmap];0.97[LWK][hapmap];0.91[YRI][hapmap]
rs6665194	0.81[LWK][hapmap]
rs971173	0.86[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1217414	PTPN22	cis	parietal	SCAN
rs1217414	PHTF1	cis	cerebellum	SCAN
rs1217414	AP4B1	cis	cerebellum	SCAN
rs1217414	RAP1A	cis	parietal	SCAN
rs1217414	FAM40A	cis	parietal	SCAN
rs1217414	BCL2L15	cis	cerebellum	SCAN
rs1217414	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:114405800-114413800	Weak transcription	K562	blood
3	chr1:114410000-114417800	Enhancers	NHEK	skin
4	chr1:114410200-114413200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:114410600-114413800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr1:114410800-114413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:114410800-114415600	Enhancers	HMEC	breast
8	chr1:114411400-114412800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:114411400-114414000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:114411400-114414000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:114411400-114414000	Weak transcription	NH-A	brain
12	chr1:114411400-114414000	Weak transcription	NHDF-Ad	bronchial
13	chr1:114411400-114414400	Active TSS	GM12878-XiMat	blood
14	chr1:114411400-114414600	Weak transcription	Small Intestine	intestine
15	chr1:114411600-114412800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:114411600-114414000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:114411600-114414000	Weak transcription	Osteobl	bone
18	chr1:114411600-114414200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:114411800-114413400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:114411800-114413600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:114411800-114413800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr1:114411800-114414200	Weak transcription	HUVEC	blood vessel
23	chr1:114412000-114414000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:114412000-114414000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:114412000-114415200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr1:114412000-114415600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr1:114412200-114412800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr1:114412200-114412800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:114412400-114412800	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:114412400-114412800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:114412400-114412800	Active TSS	Colonic Mucosa	Colon
32	chr1:114412400-114412800	Flanking Active TSS	Thymus	Thymus
33	chr1:114412400-114413000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:114412400-114413000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:114412400-114413200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr1:114412400-114413400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr1:114412400-114413400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr1:114412400-114413600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:114412400-114413600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:114412400-114414000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:114412400-114414600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr1:114412400-114415600	Flanking Active TSS	Dnd41	blood
43	chr1:114412600-114413000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:114412600-114413000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:114412600-114413000	Active TSS	Fetal Thymus	thymus
46	chr1:114412600-114413400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:114412600-114414000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:114412600-114414600	Active TSS	Duodenum Mucosa	Duodenum
49	chr1:114412600-114415600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:114412600-114416000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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