Variant report

Variant	rs28622917
Chromosome Location	chr3:133894761-133894762
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	chr3:133894692..133896687-chr3:134204158..134205758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11711122	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716232	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13059653	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065669	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13067053	0.82[EUR][1000 genomes]
rs13073076	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13074310	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075472	0.89[EUR][1000 genomes]
rs13080318	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13080570	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13096460	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28450327	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28484700	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28667241	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28726214	0.82[EUR][1000 genomes]
rs28785783	0.91[EUR][1000 genomes]
rs28852473	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34678092	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35241315	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35293292	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35338993	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35397189	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35702871	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35750568	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077107	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241373	0.89[EUR][1000 genomes]
rs4241374	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4280634	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4305420	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4342102	0.86[EUR][1000 genomes]
rs4345064	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4355279	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4380411	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4413311	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4419375	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4450812	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4507252	0.89[EUR][1000 genomes]
rs4507253	0.89[EUR][1000 genomes]
rs4546144	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547696	0.86[EUR][1000 genomes]
rs4552343	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4558752	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4640559	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4854611	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854614	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854615	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854811	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4854812	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854817	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854818	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854820	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854825	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57457165	0.80[AFR][1000 genomes]
rs61598143	0.80[AFR][1000 genomes]
rs62269301	0.86[EUR][1000 genomes]
rs6439460	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439461	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776592	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777817	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796570	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6802495	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611109	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613782	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7626852	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7632489	0.89[EUR][1000 genomes]
rs7632556	0.89[EUR][1000 genomes]
rs7632691	0.89[EUR][1000 genomes]
rs7653175	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289460	0.86[EUR][1000 genomes]
rs9790149	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827105	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9831998	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842531	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9843541	0.86[EUR][1000 genomes]
rs9847033	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850689	0.89[EUR][1000 genomes]
rs9853047	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9857486	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9857977	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9865639	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9867748	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9869195	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869613	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870910	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9871137	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9877506	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878348	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882875	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133863000-133902200	Weak transcription	GM12878-XiMat	blood
2	chr3:133864200-133899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:133866200-133898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:133871800-133919200	Weak transcription	K562	blood
5	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
8	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
10	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
11	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
12	chr3:133878200-133901600	Weak transcription	Fetal Brain Male	brain
13	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:133881800-133908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:133882400-133897400	Weak transcription	Fetal Kidney	kidney
16	chr3:133884600-133900000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:133885000-133902400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:133885600-133897800	Weak transcription	A549	lung
19	chr3:133885600-133907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:133886800-133896400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:133887200-133897000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:133887600-133895000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:133887600-133895200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:133887600-133896600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:133887600-133900400	Strong transcription	Primary T cells from cord blood	blood
27	chr3:133887600-133902800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:133887600-133903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:133887800-133895200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:133887800-133897400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:133887800-133900800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:133887800-133900800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:133888000-133896600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:133888000-133901000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:133888200-133896600	Strong transcription	HMEC	breast
36	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
37	chr3:133888600-133896600	Strong transcription	Osteobl	bone
38	chr3:133888600-133905400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:133888800-133895200	Strong transcription	Adipose Nuclei	Adipose
40	chr3:133889000-133895200	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:133889000-133896600	Strong transcription	NH-A	brain
42	chr3:133889200-133895200	Strong transcription	Liver	Liver
43	chr3:133889200-133895600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:133889200-133895600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:133889200-133895800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:133889200-133896400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:133889200-133896600	Strong transcription	Fetal Intestine Large	intestine
48	chr3:133889800-133895400	Weak transcription	Stomach Mucosa	stomach
49	chr3:133890200-133895000	Strong transcription	Fetal Stomach	stomach
50	chr3:133890400-133895800	Strong transcription	Fetal Intestine Small	intestine

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