Variant report

Variant	rs55872019
Chromosome Location	chr3:51653867-51653868
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	chr3:51650428..51652785-chr3:51653389..51655830,3	K562	blood:
2	chr3:51571369..51573938-chr3:51651321..51654419,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11553574	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12485610	0.81[EUR][1000 genomes]
rs12485825	0.92[ASN][1000 genomes]
rs12486568	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487426	0.81[EUR][1000 genomes]
rs12490471	0.81[EUR][1000 genomes]
rs12492624	0.81[EUR][1000 genomes]
rs12493265	0.81[EUR][1000 genomes]
rs12493857	0.81[EUR][1000 genomes]
rs12494462	0.81[EUR][1000 genomes]
rs12496340	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13324384	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051811	0.81[EUR][1000 genomes]
rs2082992	0.81[EUR][1000 genomes]
rs2082993	0.81[EUR][1000 genomes]
rs35536327	0.81[EUR][1000 genomes]
rs4687553	0.81[EUR][1000 genomes]
rs4687563	0.81[EUR][1000 genomes]
rs4687592	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687599	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687605	0.81[EUR][1000 genomes]
rs4687656	0.81[EUR][1000 genomes]
rs4687691	0.81[EUR][1000 genomes]
rs4687769	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687794	0.81[EUR][1000 genomes]
rs55667499	0.81[EUR][1000 genomes]
rs55706150	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58059174	0.81[EUR][1000 genomes]
rs58189274	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58762652	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59564034	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60007226	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60606339	0.81[EUR][1000 genomes]
rs61689323	0.81[EUR][1000 genomes]
rs72951443	0.81[EUR][1000 genomes]
rs72951490	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7375146	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73834258	0.81[EUR][1000 genomes]
rs73834265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73834273	0.80[AFR][1000 genomes]
rs73834274	0.80[AFR][1000 genomes]
rs73834276	0.80[AFR][1000 genomes]
rs9827186	0.81[EUR][1000 genomes]
rs9842600	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51600800-51654600	Weak transcription	Stomach Mucosa	stomach
2	chr3:51625200-51655400	Weak transcription	Gastric	stomach
3	chr3:51625400-51663400	Weak transcription	Right Ventricle	heart
4	chr3:51625600-51654000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:51625600-51654000	Weak transcription	Ovary	ovary
6	chr3:51625600-51655400	Weak transcription	Aorta	Aorta
7	chr3:51625600-51658200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:51625800-51654000	Weak transcription	Left Ventricle	heart
9	chr3:51625800-51655200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:51625800-51655400	Weak transcription	Lung	lung
11	chr3:51625800-51655800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:51626000-51654600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:51626000-51656600	Weak transcription	Placenta	Placenta
14	chr3:51628800-51660800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:51629800-51654000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:51629800-51655200	Weak transcription	Fetal Lung	lung
17	chr3:51630400-51661400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:51630800-51661400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:51631000-51655400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:51631000-51661400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:51631000-51661600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:51631000-51661600	Weak transcription	Fetal Thymus	thymus
23	chr3:51631800-51660800	Weak transcription	Primary B cells from cord blood	blood
24	chr3:51633000-51655800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:51634600-51655200	Weak transcription	Fetal Stomach	stomach
26	chr3:51636200-51661200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:51636600-51655200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:51637600-51660800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:51640200-51656400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:51640600-51654600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:51640600-51655200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:51640600-51661000	Weak transcription	Dnd41	blood
33	chr3:51640600-51661200	Weak transcription	Thymus	Thymus
34	chr3:51640600-51663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:51640800-51654000	Weak transcription	Primary T cells from cord blood	blood
36	chr3:51643000-51654600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:51643000-51660800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:51643400-51655400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:51643600-51656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:51643800-51661000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:51643800-51661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:51645000-51655200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:51646200-51655400	Weak transcription	Hela-S3	cervix
44	chr3:51648800-51656400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:51649800-51663400	Weak transcription	GM12878-XiMat	blood
46	chr3:51650400-51657600	Enhancers	Liver	Liver
47	chr3:51651200-51656200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:51651400-51655800	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:51651800-51656800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:51652400-51656600	Enhancers	HepG2	liver

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