Variant report

Variant	rs55930449
Chromosome Location	chr3:159994587-159994588
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	chr3:159990099..159991840-chr3:159992941..159995027,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1141023	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17236389	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17236452	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17236487	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17826161	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979160	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2029361	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2152424	0.92[ASN][1000 genomes]
rs35281166	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3737214	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41272955	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272957	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254702	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679883	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679887	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4680577	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680582	0.85[ASN][1000 genomes]
rs4680590	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55853078	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56030166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56051094	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56322040	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6776582	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154549	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154552	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73154567	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154591	0.85[ASN][1000 genomes]
rs73154596	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73154600	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73154602	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73155903	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73155920	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73155922	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7622031	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159971800-160009600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:159972600-160009400	Weak transcription	Fetal Stomach	stomach
4	chr3:159972800-159999000	Weak transcription	Aorta	Aorta
5	chr3:159973400-159994600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
7	chr3:159974600-159999600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:159974800-160014400	Weak transcription	HSMM	muscle
9	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
11	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
12	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:159975600-160009600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:159976600-159995800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:159977600-159996000	Weak transcription	Left Ventricle	heart
18	chr3:159977800-160014400	Weak transcription	NHDF-Ad	bronchial
19	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:159978800-159999000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:159978800-159999200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:159979000-160007800	Weak transcription	Liver	Liver
23	chr3:159979200-159999000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:159979600-160003400	Weak transcription	Hela-S3	cervix
25	chr3:159981200-159996000	Weak transcription	Fetal Lung	lung
26	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
27	chr3:159983000-159996800	Weak transcription	GM12878-XiMat	blood
28	chr3:159983000-160009400	Weak transcription	Pancreas	Pancrea
29	chr3:159983200-159997000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:159983200-160000800	Weak transcription	Psoas Muscle	Psoas
31	chr3:159983400-160009400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:159983400-160014200	Weak transcription	HSMMtube	muscle
33	chr3:159983600-159999000	Weak transcription	Lung	lung
34	chr3:159983600-160020400	Weak transcription	Brain Germinal Matrix	brain
35	chr3:159983800-160001400	Weak transcription	Brain Substantia Nigra	brain
36	chr3:159984200-159998800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:159984400-159995800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:159984600-160014600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:159985000-159996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:159985200-159997200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr3:159985800-159998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:159985800-160011600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:159986000-160009200	Weak transcription	Thymus	Thymus
45	chr3:159986000-160009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:159986400-160009600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:159986400-160024800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:159987000-160014400	Weak transcription	NHLF	lung
49	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:159988800-160004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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