Variant report

Variant	rs34877889
Chromosome Location	chr1:114396369-114396370
allele	A/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: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10127930	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10489936	0.86[EUR][1000 genomes]
rs1080307	0.86[EUR][1000 genomes]
rs1217384	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12723023	0.81[EUR][1000 genomes]
rs12729708	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730735	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731010	0.84[EUR][1000 genomes]
rs12734625	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12735104	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12739970	0.81[EUR][1000 genomes]
rs12746609	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12748727	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12752932	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12753075	0.82[EUR][1000 genomes]
rs12753351	0.86[EUR][1000 genomes]
rs12758546	0.87[EUR][1000 genomes]
rs12760457	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13374352	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17274550	0.87[EUR][1000 genomes]
rs17274620	0.87[EUR][1000 genomes]
rs17274634	0.87[EUR][1000 genomes]
rs17359302	0.87[EUR][1000 genomes]
rs17462614	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17509390	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1885454	0.87[EUR][1000 genomes]
rs2040040	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2359173	0.87[EUR][1000 genomes]
rs2359174	0.87[EUR][1000 genomes]
rs34042871	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34341173	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34649199	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34698891	0.86[EUR][1000 genomes]
rs34857922	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35320278	0.87[EUR][1000 genomes]
rs35383900	0.86[EUR][1000 genomes]
rs35836713	0.87[EUR][1000 genomes]
rs36115604	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747998	0.87[EUR][1000 genomes]
rs3748003	0.87[EUR][1000 genomes]
rs3761931	0.86[EUR][1000 genomes]
rs3789595	0.87[EUR][1000 genomes]
rs3789607	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817579	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61817586	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817617	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819423	0.82[EUR][1000 genomes]
rs61819424	0.80[EUR][1000 genomes]
rs61820162	0.86[EUR][1000 genomes]
rs6668829	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674848	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6703387	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71662845	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7533391	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533605	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549685	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7555354	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803891	0.84[EUR][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

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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