Variant report

Variant	rs1217382
Chromosome Location	chr1:114423653-114423654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10745340	0.87[YRI][hapmap]
rs10776775	0.87[YRI][hapmap]
rs10858022	0.87[YRI][hapmap]
rs11102678	0.90[JPT][hapmap]
rs11102695	0.86[CEU][hapmap]
rs1217375	0.90[JPT][hapmap]
rs1217391	0.86[YRI][hapmap]
rs1217392	0.87[YRI][hapmap]
rs1217393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217397	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217400	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217403	0.90[JPT][hapmap]
rs1217408	0.90[JPT][hapmap]
rs1217414	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs1217423	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230681	0.90[JPT][hapmap]
rs1310183	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464525	0.87[YRI][hapmap]
rs1746860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935836	0.90[JPT][hapmap]
rs1970559	0.90[JPT][hapmap]
rs2040041	0.90[JPT][hapmap]
rs2185827	0.90[JPT][hapmap]
rs2476599	0.90[JPT][hapmap]
rs2476602	0.90[JPT][hapmap]
rs3789597	0.90[JPT][hapmap]
rs3789613	0.87[YRI][hapmap]
rs6661817	0.87[YRI][hapmap]
rs7523862	0.87[YRI][hapmap]
rs7524200	0.85[YRI][hapmap]
rs971173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1217382	MAGI3	cis	cerebellum	SCAN
rs1217382	AP4B1	cis	cerebellum	SCAN
rs1217382	BCL2L15	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114415400-114428800	Weak transcription	Colonic Mucosa	Colon
3	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
4	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
5	chr1:114417600-114428800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:114419000-114427800	Weak transcription	Pancreas	Pancrea
7	chr1:114420200-114437800	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
9	chr1:114421000-114424200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:114421000-114424600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:114421000-114424600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:114421000-114424800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:114421200-114424400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:114421600-114424000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:114421600-114424600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:114421600-114424600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:114421800-114424800	Enhancers	Dnd41	blood
18	chr1:114421800-114429600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:114422000-114424000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:114422200-114423800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:114422400-114423800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:114422400-114424000	Weak transcription	Fetal Intestine Large	intestine
23	chr1:114422400-114429000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:114422600-114424000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:114422600-114424200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:114422600-114424200	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:114422800-114423800	Weak transcription	Small Intestine	intestine
28	chr1:114422800-114424200	Weak transcription	Fetal Intestine Small	intestine
29	chr1:114422800-114429000	Weak transcription	Fetal Stomach	stomach
30	chr1:114423000-114428000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:114423200-114423800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:114423200-114424000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr1:114423200-114424200	Enhancers	Primary T cells from cord blood	blood
34	chr1:114423200-114424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:114423400-114423800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:114423400-114423800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:114423400-114424000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:114423400-114424000	Enhancers	Fetal Lung	lung
39	chr1:114423400-114424000	Enhancers	HUVEC	blood vessel
40	chr1:114423400-114424200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:114423400-114424600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:114423400-114424600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:114423400-114429600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:114423600-114424000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:114423600-114424600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:114423600-114424600	Enhancers	Stomach Mucosa	stomach
47	chr1:114423600-114425000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:114423600-114436000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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