Variant report

Variant	rs1217408
Chromosome Location	chr1:114396280-114396281
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: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11102678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1146183	0.85[CHB][hapmap]
rs1146184	0.85[CHB][hapmap]
rs1146185	0.84[CHB][hapmap]
rs1217375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1217378	0.80[AFR][1000 genomes]
rs1217379	0.83[YRI][hapmap]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.91[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217404	0.83[AFR][1000 genomes]
rs1217405	0.90[AFR][1000 genomes]
rs1217406	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1217414	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	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1217418	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1217419	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1217420	0.81[AFR][1000 genomes]
rs1217423	0.82[JPT][hapmap]
rs1230681	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1230684	0.89[ASN][1000 genomes]
rs1310182	0.92[AFR][1000 genomes]
rs13524	0.85[CHB][hapmap];0.83[YRI][hapmap]
rs1746857	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1970559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040041	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2185827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2476599	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2476600	0.83[YRI][hapmap]
rs2476602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476604	0.90[AFR][1000 genomes]
rs2636000	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2797416	0.83[YRI][hapmap]
rs3789597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3789598	0.91[YRI][hapmap]
rs3789600	0.96[YRI][hapmap]
rs4991898	0.83[AFR][1000 genomes]
rs6537798	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs7555634	0.83[YRI][hapmap]
rs971173	0.90[JPT][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

No data

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	chr1:114391000-114396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:114391200-114397000	Weak transcription	Fetal Thymus	thymus
10	chr1:114391200-114401800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:114391400-114396800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:114391400-114396800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:114393200-114396800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:114393200-114397000	Weak transcription	Dnd41	blood
15	chr1:114393400-114396800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:114393600-114397000	Weak transcription	Primary B cells from cord blood	blood
17	chr1:114393600-114399400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:114393800-114397000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:114393800-114397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:114393800-114397000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:114394200-114396800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:114394200-114397000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:114394200-114397000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:114394200-114399200	Strong transcription	GM12878-XiMat	blood
25	chr1:114394400-114397000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:114395000-114396800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:114395000-114396800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:114395400-114396800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:114395400-114396800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:114395600-114396400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:114395600-114396800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:114395800-114396600	Weak transcription	Thymus	Thymus
34	chr1:114395800-114396600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:114395800-114397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:114395800-114398600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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