Variant report

Variant	rs11582409
Chromosome Location	chr1:114399433-114399434
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	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10745340	0.85[YRI][hapmap]
rs10776775	0.85[YRI][hapmap]
rs10858022	0.85[YRI][hapmap]
rs11584821	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1217391	0.85[YRI][hapmap]
rs1217392	0.85[YRI][hapmap]
rs17031795	0.84[ASN][1000 genomes]
rs17274627	0.91[CHB][hapmap]
rs17463292	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17464525	0.85[YRI][hapmap]
rs17509844	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17510162	0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3195954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34122108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35173468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761935	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789604	0.83[CEU][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789608	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789613	0.85[YRI][hapmap]
rs3811021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4393155	0.86[ASN][1000 genomes]
rs4589108	0.84[ASN][1000 genomes]
rs4839000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4839333	0.91[CHB][hapmap]
rs4839341	0.84[ASN][1000 genomes]
rs4839346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55646484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55940960	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55951516	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537796	0.85[YRI][hapmap]
rs6658523	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661817	0.85[YRI][hapmap]
rs6700802	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7523862	0.85[YRI][hapmap]
rs7524200	0.82[YRI][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11582409	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 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	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:114378000-114402600	Weak transcription	Colonic Mucosa	Colon
5	chr1:114390800-114400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:114391200-114401800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:114394400-114402200	Strong transcription	Primary T cells from cord blood	blood
8	chr1:114396400-114400800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:114396600-114401600	Strong transcription	Thymus	Thymus
10	chr1:114396800-114401600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:114396800-114401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:114396800-114402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:114396800-114402000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:114396800-114402200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:114397000-114400000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:114397000-114401600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:114397000-114401800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:114397000-114401800	Strong transcription	Fetal Thymus	thymus
19	chr1:114397000-114402400	Strong transcription	Dnd41	blood
20	chr1:114397200-114399600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:114397400-114402000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:114397600-114402600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:114397800-114400000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:114397800-114401800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr1:114397800-114402000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:114397800-114409800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:114398400-114399600	Enhancers	Adipose Nuclei	Adipose
28	chr1:114398400-114399600	Enhancers	HepG2	liver
29	chr1:114398400-114399800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:114398600-114399800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:114399200-114400200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:114399200-114402600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:114399200-114402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:114399400-114399600	Weak transcription	GM12878-XiMat	blood
35	chr1:114399400-114400000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:114399400-114400000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:114399400-114400200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:114399400-114400200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:114399400-114401800	Enhancers	Primary B cells from cord blood	blood
40	chr1:114399400-114401800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:114399400-114401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:114399400-114402000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:114399400-114402000	Weak transcription	NHEK	skin
44	chr1:114399400-114402200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:114399400-114402200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:114399400-114402600	Weak transcription	HSMM	muscle
47	chr1:114399400-114403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:114399400-114403200	Weak transcription	HSMMtube	muscle

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