Variant report

Variant	rs6042080
Chromosome Location	chr20:13391323-13391324
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	chr20:13389415..13391531-chr20:13398502..13400479,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12480266	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12480276	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2038437	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2145139	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2145140	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2327755	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28867078	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55940819	0.83[EUR][1000 genomes]
rs57675086	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57873080	0.82[EUR][1000 genomes]
rs58023165	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58129464	0.85[EUR][1000 genomes]
rs59051161	0.85[EUR][1000 genomes]
rs59299264	0.82[EUR][1000 genomes]
rs6033689	0.84[AMR][1000 genomes]
rs6033693	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6033694	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6033695	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6033699	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033702	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6033703	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033704	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033706	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033708	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033712	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6042061	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042063	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042068	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042075	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6042076	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042077	0.85[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6042079	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6042081	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6042082	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042083	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042084	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042086	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042089	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042105	0.83[AMR][1000 genomes]
rs6042113	0.82[EUR][1000 genomes]
rs6042121	0.82[EUR][1000 genomes]
rs6042145	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs6042151	0.83[AMR][1000 genomes]
rs6042152	0.82[EUR][1000 genomes]
rs6105088	0.85[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6105089	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6105091	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6105092	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105093	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105094	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105095	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6109848	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6109849	0.94[AMR][1000 genomes]
rs6109850	0.82[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6109859	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6109863	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6109866	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs6109867	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6109868	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6109869	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs6109870	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6109871	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109872	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6109873	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109882	0.83[AMR][1000 genomes]
rs6109886	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6109888	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6109895	0.82[CEU][hapmap]
rs6109902	0.82[EUR][1000 genomes]
rs6109904	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs61151551	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61612076	0.85[EUR][1000 genomes]
rs73901179	0.82[EUR][1000 genomes]
rs8121784	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs927122	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[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	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 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	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
2	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13368600-13397400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr20:13368800-13392200	Weak transcription	Aorta	Aorta
5	chr20:13369000-13411200	Strong transcription	Dnd41	blood
6	chr20:13369400-13397000	Weak transcription	Primary B cells from cord blood	blood
7	chr20:13369400-13397200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr20:13369600-13397000	Weak transcription	Fetal Thymus	thymus
9	chr20:13371400-13413600	Weak transcription	Ovary	ovary
10	chr20:13371800-13397200	Weak transcription	Primary T cells from cord blood	blood
11	chr20:13372000-13395800	Weak transcription	HepG2	liver
12	chr20:13372000-13396400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr20:13372000-13397400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr20:13372000-13397400	Weak transcription	Left Ventricle	heart
15	chr20:13372000-13397400	Weak transcription	Thymus	Thymus
16	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:13374400-13410800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:13374600-13397400	Weak transcription	Fetal Intestine Small	intestine
19	chr20:13374600-13399400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr20:13374600-13405800	Weak transcription	Fetal Stomach	stomach
21	chr20:13379000-13410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:13379200-13463000	Weak transcription	HSMM	muscle
23	chr20:13380800-13397600	Weak transcription	Fetal Lung	lung
24	chr20:13383200-13392200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:13383200-13393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:13383200-13397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:13383400-13392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:13383600-13391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr20:13383600-13393400	Weak transcription	HMEC	breast
30	chr20:13383800-13392200	Weak transcription	NHEK	skin
31	chr20:13385200-13397400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:13387800-13397600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr20:13390800-13393400	Weak transcription	Liver	Liver
34	chr20:13390800-13397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:13390800-13403000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr20:13391200-13403400	Weak transcription	Fetal Kidney	kidney

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