Variant report

Variant	rs6109877
Chromosome Location	chr20:13410135-13410136
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	chr20:13408378..13410884-chr20:13417652..13421238,3	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs12329620	0.82[EUR][1000 genomes]
rs12480266	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12480276	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2008702	0.82[EUR][1000 genomes]
rs2038437	0.97[EUR][1000 genomes]
rs2145139	0.89[EUR][1000 genomes]
rs2145140	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2327755	0.94[EUR][1000 genomes]
rs57675086	0.94[EUR][1000 genomes]
rs57873080	0.97[EUR][1000 genomes]
rs58023165	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs58129464	0.94[EUR][1000 genomes]
rs59051161	0.94[EUR][1000 genomes]
rs59299264	0.97[EUR][1000 genomes]
rs59388287	0.82[EUR][1000 genomes]
rs6033693	0.94[EUR][1000 genomes]
rs6033694	0.94[EUR][1000 genomes]
rs6033695	0.94[EUR][1000 genomes]
rs6033699	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6033702	0.97[EUR][1000 genomes]
rs6033703	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6033704	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6033706	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6033708	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6033712	0.97[EUR][1000 genomes]
rs6033714	0.82[EUR][1000 genomes]
rs6033718	0.82[EUR][1000 genomes]
rs6042075	0.94[EUR][1000 genomes]
rs6042077	0.94[EUR][1000 genomes]
rs6042079	0.94[EUR][1000 genomes]
rs6042081	0.97[EUR][1000 genomes]
rs6042082	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042083	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042084	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042086	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042087	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042089	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6042093	0.82[EUR][1000 genomes]
rs6042101	0.82[EUR][1000 genomes]
rs6042107	0.82[EUR][1000 genomes]
rs6042108	0.82[EUR][1000 genomes]
rs6042111	0.82[EUR][1000 genomes]
rs6042113	0.97[EUR][1000 genomes]
rs6042116	0.82[EUR][1000 genomes]
rs6042121	0.97[EUR][1000 genomes]
rs6042123	0.82[EUR][1000 genomes]
rs6042130	0.82[EUR][1000 genomes]
rs6042136	0.82[EUR][1000 genomes]
rs6042152	0.97[EUR][1000 genomes]
rs6042154	0.82[EUR][1000 genomes]
rs6105088	0.94[EUR][1000 genomes]
rs6105089	0.94[EUR][1000 genomes]
rs6105091	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6105092	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6105093	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6105094	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6105095	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6105097	0.82[EUR][1000 genomes]
rs6105105	0.82[EUR][1000 genomes]
rs6105108	0.82[EUR][1000 genomes]
rs6105109	0.82[EUR][1000 genomes]
rs6109859	0.94[EUR][1000 genomes]
rs6109863	0.94[EUR][1000 genomes]
rs6109866	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6109867	0.82[EUR][1000 genomes]
rs6109868	0.97[EUR][1000 genomes]
rs6109869	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6109870	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6109871	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6109872	0.97[EUR][1000 genomes]
rs6109873	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6109879	0.82[EUR][1000 genomes]
rs6109883	0.82[EUR][1000 genomes]
rs6109886	0.97[EUR][1000 genomes]
rs6109888	0.97[EUR][1000 genomes]
rs6109889	0.82[EUR][1000 genomes]
rs6109895	0.82[EUR][1000 genomes]
rs6109900	0.82[EUR][1000 genomes]
rs6109901	0.82[EUR][1000 genomes]
rs6109902	0.97[EUR][1000 genomes]
rs6109904	0.97[EUR][1000 genomes]
rs61151551	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61518689	0.82[EUR][1000 genomes]
rs61612076	0.94[EUR][1000 genomes]
rs73901179	0.97[EUR][1000 genomes]
rs8119260	0.82[EUR][1000 genomes]
rs927122	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9653627	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv174307	chr20:13410135-13410135	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

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	chr20:13369000-13411200	Strong transcription	Dnd41	blood
4	chr20:13371400-13413600	Weak transcription	Ovary	ovary
5	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:13374400-13410800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr20:13379000-13410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:13379200-13463000	Weak transcription	HSMM	muscle
9	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
10	chr20:13392800-13415000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:13393800-13411000	Weak transcription	Pancreas	Pancrea
12	chr20:13393800-13416800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr20:13394000-13415600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:13394200-13416800	Weak transcription	Esophagus	oesophagus
15	chr20:13394200-13417200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr20:13395000-13415000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:13395400-13411000	Weak transcription	Spleen	Spleen
18	chr20:13395600-13416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr20:13395600-13477800	Weak transcription	Gastric	stomach
20	chr20:13396000-13410600	Weak transcription	GM12878-XiMat	blood
21	chr20:13396000-13415000	Weak transcription	Brain Hippocampus Middle	brain
22	chr20:13396000-13417000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr20:13397600-13410600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:13397800-13414400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr20:13397800-13415000	Weak transcription	Adipose Nuclei	Adipose
27	chr20:13398000-13410800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr20:13398000-13411000	Weak transcription	Primary B cells from cord blood	blood
29	chr20:13398200-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:13398200-13410200	Weak transcription	Thymus	Thymus
31	chr20:13398200-13410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr20:13398200-13411000	Weak transcription	Lung	lung
33	chr20:13398200-13412000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr20:13398200-13414600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:13398200-13415000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr20:13398200-13415000	Weak transcription	Aorta	Aorta
37	chr20:13398200-13415000	Weak transcription	Fetal Intestine Small	intestine
38	chr20:13398200-13415000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr20:13398200-13415000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr20:13398200-13416800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr20:13398200-13417800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr20:13399600-13410800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr20:13399800-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:13399800-13430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr20:13400600-13411000	Weak transcription	Placenta	Placenta
46	chr20:13403600-13410400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr20:13403800-13435000	Weak transcription	HMEC	breast
48	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:13404400-13434800	Weak transcription	NHEK	skin
50	chr20:13405400-13415000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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