Variant report

Variant	rs55924660
Chromosome Location	chr2:20086343-20086344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20085889..20088843-chr2:20102352..20104719,3	MCF-7	breast:
2	chr2:20070422..20073365-chr2:20086034..20088934,3	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3731661	0.82[ASN][1000 genomes]
rs62109396	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62109400	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62109407	0.82[ASN][1000 genomes]
rs62109409	0.82[ASN][1000 genomes]
rs72779339	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72779347	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7587014	0.82[ASN][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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
2	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
3	chr2:20069600-20087800	Weak transcription	Gastric	stomach
4	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
6	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:20076600-20087000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
15	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
17	chr2:20079200-20087000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:20079400-20097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
21	chr2:20081800-20095200	Weak transcription	Primary T cells from cord blood	blood
22	chr2:20082600-20087800	Weak transcription	Left Ventricle	heart
23	chr2:20083000-20095400	Weak transcription	Fetal Brain Female	brain
24	chr2:20085600-20086600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:20085600-20086800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:20085600-20087000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:20085600-20088600	Weak transcription	Right Ventricle	heart
28	chr2:20085800-20086600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:20085800-20086600	Enhancers	HSMMtube	muscle
30	chr2:20085800-20090000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:20086000-20086600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:20086000-20086600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:20086000-20086600	Enhancers	NHEK	skin
34	chr2:20086200-20086600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:20086200-20086600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:20086200-20086600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:20086200-20086600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:20086200-20086600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:20086200-20086600	Enhancers	Psoas Muscle	Psoas
40	chr2:20086200-20086600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr2:20086200-20086600	Enhancers	Spleen	Spleen
42	chr2:20086200-20086600	Enhancers	HMEC	breast
43	chr2:20086200-20087000	Enhancers	Skeletal Muscle Female	skeletal muscle

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