Variant report

Variant	rs1217410
Chromosome Location	chr1:114396816-114396817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114396276..114399054-chr1:114408644..114411228,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10858017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10858018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10858019	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10858021	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102661	0.80[EUR][1000 genomes]
rs11102669	0.86[EUR][1000 genomes]
rs11102689	0.85[EUR][1000 genomes]
rs11102691	0.95[CEU][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1146182	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs1146187	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs12041547	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044534	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12060836	0.85[YRI][hapmap]
rs12061482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12063216	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12069381	0.85[YRI][hapmap]
rs12071676	0.85[YRI][hapmap]
rs12094790	0.85[YRI][hapmap]
rs1217192	0.80[EUR][1000 genomes]
rs1217193	0.80[EUR][1000 genomes]
rs1217200	0.80[EUR][1000 genomes]
rs1217210	0.86[EUR][1000 genomes]
rs1217376	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217386	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217407	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217413	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]
rs1217415	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1217416	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230637	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230638	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1230639	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1230640	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230642	0.81[ASN][1000 genomes]
rs1230645	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230646	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230647	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230649	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230655	0.86[EUR][1000 genomes]
rs1230656	0.80[EUR][1000 genomes]
rs1230658	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs1230659	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs1230663	0.82[EUR][1000 genomes]
rs1230671	0.86[EUR][1000 genomes]
rs1230678	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230679	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230683	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1230685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230687	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1237682	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565589	0.80[EUR][1000 genomes]
rs12566340	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599971	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1743605	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1746853	0.81[CHB][hapmap]
rs1775754	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777234	0.83[EUR][1000 genomes]
rs1777237	0.86[EUR][1000 genomes]
rs1777238	0.86[EUR][1000 genomes]
rs1777241	0.86[EUR][1000 genomes]
rs1935838	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1936398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093436	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2243471	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2295853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358816	0.81[JPT][hapmap]
rs2359167	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2488457	0.90[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2488458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636014	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797408	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2797409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2797412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2798135	0.85[EUR][1000 genomes]
rs2798138	0.85[EUR][1000 genomes]
rs4145859	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4423005	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4565712	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4838997	0.87[EUR][1000 genomes]
rs4838998	0.82[ASN][1000 genomes]
rs4839335	0.88[EUR][1000 genomes]
rs61817589	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537792	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs6537795	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6663679	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6698586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7526209	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7529353	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553188	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9429730	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.95[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1217410	MAGI3	cis	cerebellum	SCAN
rs1217410	CAPZA1	cis	parietal	SCAN
rs1217410	MAGI3	cis	parietal	SCAN
rs1217410	PHTF1	cis	parietal	SCAN
rs1217410	PHTF1	cis	cerebellum	SCAN
rs1217410	BCL2L15	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:114378000-114402600	Weak transcription	Colonic Mucosa	Colon
6	chr1:114390600-114397000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:114390800-114400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:114391200-114397000	Weak transcription	Fetal Thymus	thymus
9	chr1:114391200-114401800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:114393200-114397000	Weak transcription	Dnd41	blood
11	chr1:114393600-114397000	Weak transcription	Primary B cells from cord blood	blood
12	chr1:114393600-114399400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:114393800-114397000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:114393800-114397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:114393800-114397000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:114394200-114397000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:114394200-114397000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:114394200-114399200	Strong transcription	GM12878-XiMat	blood
19	chr1:114394400-114397000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
21	chr1:114395800-114397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:114395800-114398600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:114396400-114400800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:114396600-114397200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:114396600-114399400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:114396600-114401600	Strong transcription	Thymus	Thymus
27	chr1:114396800-114397400	Genic enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:114396800-114397800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:114396800-114399200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:114396800-114399400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:114396800-114399400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:114396800-114401600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:114396800-114401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:114396800-114402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:114396800-114402000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:114396800-114402200	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links