Variant report

Variant	rs55820558
Chromosome Location	chr4:148820116-148820117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148812422..148814436-chr4:148818946..148820969,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10000278	0.92[EUR][1000 genomes]
rs10001688	0.92[EUR][1000 genomes]
rs10001756	0.94[EUR][1000 genomes]
rs10003507	0.92[EUR][1000 genomes]
rs10004138	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10004691	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10004792	0.92[EUR][1000 genomes]
rs10014593	0.92[EUR][1000 genomes]
rs10014696	0.92[EUR][1000 genomes]
rs10015875	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025069	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10026985	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10030358	0.92[EUR][1000 genomes]
rs10049932	0.92[EUR][1000 genomes]
rs11099671	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11099672	0.92[EUR][1000 genomes]
rs11734553	0.89[EUR][1000 genomes]
rs11735412	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12331562	0.92[EUR][1000 genomes]
rs12509618	0.89[EUR][1000 genomes]
rs12513192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643550	0.92[EUR][1000 genomes]
rs13129325	0.92[EUR][1000 genomes]
rs13151898	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369958	0.92[EUR][1000 genomes]
rs17024037	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17613979	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17614025	0.91[EUR][1000 genomes]
rs17676080	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2043643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043645	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28576385	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28614116	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2884400	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34970355	0.89[EUR][1000 genomes]
rs35243600	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35810358	0.94[EUR][1000 genomes]
rs35899247	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3893175	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3990920	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240341	0.94[EUR][1000 genomes]
rs4491995	0.92[EUR][1000 genomes]
rs4571312	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627844	0.89[EUR][1000 genomes]
rs4835103	0.92[EUR][1000 genomes]
rs4835109	0.92[EUR][1000 genomes]
rs4835110	0.92[EUR][1000 genomes]
rs4835469	0.85[EUR][1000 genomes]
rs55650760	0.86[EUR][1000 genomes]
rs57114670	0.93[ASN][1000 genomes]
rs62330732	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62330735	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62330737	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6535569	0.85[EUR][1000 genomes]
rs6811769	0.89[EUR][1000 genomes]
rs6818371	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6832527	0.81[EUR][1000 genomes]
rs6840771	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843392	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856273	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656471	0.82[EUR][1000 genomes]
rs7660508	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677632	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7698670	0.90[EUR][1000 genomes]
rs893033	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991741	0.88[EUR][1000 genomes]
rs9994650	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995956	0.92[EUR][1000 genomes]
rs9997027	0.92[EUR][1000 genomes]
rs9999321	0.92[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	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148777000-148823000	Weak transcription	Small Intestine	intestine
2	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
3	chr4:148794800-148824600	Weak transcription	A549	lung
4	chr4:148796800-148863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
6	chr4:148797000-148834200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:148797000-148835800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:148797400-148879600	Weak transcription	Gastric	stomach
9	chr4:148797600-148820200	Weak transcription	Osteobl	bone
10	chr4:148797600-148824600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:148801800-148830200	Weak transcription	NHEK	skin
12	chr4:148804600-148854400	Weak transcription	Psoas Muscle	Psoas
13	chr4:148805200-148824200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:148806200-148824200	Weak transcription	HSMMtube	muscle
15	chr4:148806400-148824200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:148806600-148823200	Weak transcription	Fetal Stomach	stomach
17	chr4:148806600-148824200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:148806800-148821000	Weak transcription	NHLF	lung
19	chr4:148807200-148824000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:148807800-148820200	Weak transcription	NHDF-Ad	bronchial
21	chr4:148809200-148824200	Weak transcription	Lung	lung
22	chr4:148810200-148824800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:148810400-148824200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:148810600-148829800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:148811800-148820200	Weak transcription	Left Ventricle	heart
26	chr4:148813600-148820400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:148813600-148824600	Weak transcription	Fetal Kidney	kidney
28	chr4:148813600-148827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:148814200-148822600	Weak transcription	HSMM	muscle
30	chr4:148814200-148824000	Weak transcription	Aorta	Aorta
31	chr4:148815600-148827200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:148816000-148820600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:148816000-148824200	Weak transcription	Adipose Nuclei	Adipose
34	chr4:148816200-148820200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:148816200-148820400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:148816200-148821000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:148816800-148823000	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:148817000-148824200	Weak transcription	Fetal Intestine Small	intestine
39	chr4:148817000-148827600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:148817200-148824200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:148819800-148820400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:148819800-148820600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:148820000-148820600	Enhancers	Esophagus	oesophagus
44	chr4:148820000-148820600	Enhancers	Ovary	ovary
45	chr4:148820000-148820600	Enhancers	Right Ventricle	heart
46	chr4:148820000-148822000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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