Variant report

Variant	rs1217413
Chromosome Location	chr1:114357750-114357751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114357201..114359767-chr17:56707437..56708961,2	MCF-7	breast:
2	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
3	chr1:114357090..114359689-chr1:114365164..114367947,3	K562	blood:
4	chr1:114355402..114357827-chr1:114471686..114473610,2	K562	blood:
5	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
6	chr1:114328778..114330524-chr1:114356002..114358094,2	K562	blood:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10858017	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10858018	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10858019	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10858021	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102669	0.80[EUR][1000 genomes]
rs11102691	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs1146182	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1146187	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs12041547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12044534	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12061482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12063216	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1217192	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[TSI][hapmap]
rs1217193	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs1217199	0.81[CHB][hapmap]
rs1217200	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap]
rs1217210	0.81[EUR][1000 genomes]
rs1217376	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217377	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217380	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217386	0.88[ASN][1000 genomes]
rs1217388	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217389	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217395	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217396	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1217407	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217410	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217412	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217415	0.86[CHB][hapmap];0.86[TSI][hapmap]
rs1217416	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217421	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230637	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230638	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1230639	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1230640	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230642	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230646	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230647	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230649	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230655	0.81[EUR][1000 genomes]
rs1230656	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1230658	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1230659	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1230661	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1230671	0.81[EUR][1000 genomes]
rs1230678	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230679	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230683	0.80[EUR][1000 genomes]
rs1230685	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230687	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1237682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565589	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap]
rs12566340	0.80[CHB][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1599971	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17031716	0.81[AFR][1000 genomes]
rs1743605	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1746853	0.81[CHB][hapmap]
rs1775754	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1777234	0.82[CEU][hapmap]
rs1777237	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1777238	0.81[EUR][1000 genomes]
rs1777241	0.82[CEU][hapmap];0.80[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1935838	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1936398	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981319	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2093436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2243471	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295853	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358816	0.94[CEU][hapmap]
rs2358994	1.00[ASW][hapmap]
rs2359167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488457	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488458	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2636013	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636014	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2797408	0.88[EUR][1000 genomes]
rs2797409	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797412	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761936	1.00[ASW][hapmap]
rs4145859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423005	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4565712	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4600045	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4838997	0.81[EUR][1000 genomes]
rs4839335	0.82[EUR][1000 genomes]
rs61817589	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537792	0.82[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs6537795	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6663679	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6698586	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526209	0.85[ASN][1000 genomes]
rs7529353	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7553188	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9429730	0.81[CEU][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS 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	44 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs1217413	MAGI3	cis	cerebellum	SCAN
rs1217413	CASQ2	cis	cerebellum	SCAN
rs1217413	PHTF1	cis	parietal	SCAN
rs1217413	CD58	cis	parietal	SCAN
rs1217413	SIKE1	cis	parietal	SCAN
rs1217413	PHTF1	cis	cerebellum	SCAN
rs1217413	MAGI3	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
3	chr1:114355600-114358600	Weak transcription	GM12878-XiMat	blood
4	chr1:114355800-114358200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:114355800-114361200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:114355800-114364200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:114355800-114364400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:114355800-114376600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:114355800-114376800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:114356000-114357800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:114356000-114357800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:114356000-114358400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:114356000-114358600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:114356000-114358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:114356000-114359800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:114356000-114360800	Weak transcription	Fetal Thymus	thymus
19	chr1:114356000-114362200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:114356000-114364000	Weak transcription	Thymus	Thymus
21	chr1:114356000-114370200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:114356000-114370600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:114356000-114376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:114356000-114377400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:114356200-114358000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:114356200-114358000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:114356200-114365000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:114356200-114365000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:114356200-114370200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:114356400-114359600	Weak transcription	K562	blood
31	chr1:114356400-114364400	Weak transcription	Dnd41	blood
32	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:114357200-114377600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:114357200-114377800	Strong transcription	Primary monocytes fromperipheralblood	blood

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