Variant report

Variant	rs2920143
Chromosome Location	chr11:4061352-4061353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3862693..3864773-chr11:4060192..4062998,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10742223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10767807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030841	0.80[YRI][hapmap]
rs11030853	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030907	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11604649	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12364664	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419208	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12799265	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12803023	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1372805	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304891	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412344	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2920139	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2920144	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920145	0.85[EUR][1000 genomes]
rs2923950	0.80[EUR][1000 genomes]
rs2923953	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959066	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959068	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959075	0.81[AMR][1000 genomes]
rs2959081	0.82[CHB][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs7102508	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7110060	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7116520	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7124301	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs747883	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7933164	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs9704047	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920143	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
2	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
3	chr11:4046000-4061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:4047400-4061400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:4047800-4077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:4048000-4077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:4048400-4061400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:4048400-4061800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr11:4048400-4062000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:4048400-4063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:4048400-4065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:4048600-4077800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:4049600-4070600	Weak transcription	Thymus	Thymus
14	chr11:4049800-4065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:4050200-4070800	Weak transcription	Fetal Thymus	thymus
16	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:4051200-4070200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr11:4051400-4065400	Weak transcription	Pancreas	Pancrea
19	chr11:4054800-4065000	Weak transcription	Liver	Liver
20	chr11:4055200-4061800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:4056600-4061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:4057400-4076800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:4058200-4070800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:4058800-4065400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:4058800-4065600	Weak transcription	Primary B cells from cord blood	blood
26	chr11:4058800-4070800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:4059200-4076800	Weak transcription	GM12878-XiMat	blood
28	chr11:4060000-4061400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:4060000-4061400	Weak transcription	HepG2	liver
30	chr11:4060000-4061800	Weak transcription	Psoas Muscle	Psoas
31	chr11:4060200-4061600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:4060400-4062000	Weak transcription	Primary T cells from cord blood	blood
33	chr11:4060400-4063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:4060400-4063200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:4060400-4065200	Weak transcription	NHDF-Ad	bronchial
36	chr11:4060600-4061600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:4060600-4062000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:4060600-4065200	Weak transcription	Osteobl	bone
39	chr11:4060800-4061800	Weak transcription	Ovary	ovary
40	chr11:4060800-4062800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:4060800-4065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:4061200-4062200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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