Variant report

Variant	rs6550807
Chromosome Location	chr3:23898074-23898075
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	chr3:23896966..23899460-chr3:23900307..23902326,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs4024642	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4025822	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4241514	0.82[AMR][1000 genomes]
rs4858094	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4858549	0.83[AMR][1000 genomes]
rs4858550	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4858551	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858553	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6762238	0.82[AMR][1000 genomes]
rs6764154	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7615009	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7615255	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7626431	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7627709	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648931	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651185	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845287	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9863320	0.84[AMR][1000 genomes]
rs9869299	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23855000-23900200	Weak transcription	HSMM	muscle
2	chr3:23857600-23900000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:23871200-23899000	Weak transcription	Pancreas	Pancrea
4	chr3:23876800-23906800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:23878600-23900400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:23878800-23900200	Weak transcription	Fetal Kidney	kidney
7	chr3:23879000-23898200	Weak transcription	Right Atrium	heart
8	chr3:23879000-23907400	Weak transcription	K562	blood
9	chr3:23879200-23898200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:23882200-23905600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:23882600-23900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:23882800-23906000	Weak transcription	HepG2	liver
13	chr3:23887000-23898600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:23888200-23900600	Weak transcription	Ovary	ovary
15	chr3:23890600-23902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:23892200-23900400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:23892400-23898200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:23893000-23900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:23893200-23899000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:23893600-23898200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:23893600-23898200	Weak transcription	Left Ventricle	heart
22	chr3:23893600-23898200	Weak transcription	Spleen	Spleen
23	chr3:23893600-23900200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:23893600-23900400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:23893600-23906400	Weak transcription	Aorta	Aorta
26	chr3:23893600-23906600	Weak transcription	Colonic Mucosa	Colon
27	chr3:23894000-23898200	Weak transcription	Placenta	Placenta
28	chr3:23894400-23903000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:23894600-23900800	Weak transcription	Esophagus	oesophagus
30	chr3:23894600-23902400	Weak transcription	Brain Germinal Matrix	brain
31	chr3:23894600-23903000	Weak transcription	Fetal Intestine Large	intestine
32	chr3:23894800-23900600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:23894800-23902800	Weak transcription	Fetal Intestine Small	intestine
34	chr3:23895000-23900600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:23895000-23903400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:23895400-23900600	Weak transcription	HSMMtube	muscle
37	chr3:23895600-23898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:23897400-23898600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:23897400-23898600	Enhancers	Primary B cells from cord blood	blood
40	chr3:23897400-23898600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:23897400-23898600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:23897400-23898600	Enhancers	Adipose Nuclei	Adipose
43	chr3:23897400-23898600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:23897400-23898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:23897400-23899600	Enhancers	Primary T cells from cord blood	blood
46	chr3:23897400-23901000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr3:23897400-23901200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:23897400-23901800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:23897400-23902600	Enhancers	Primary B cells from peripheral blood	blood
50	chr3:23897400-23902600	Enhancers	Thymus	Thymus

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