Variant report

Variant	rs6439460
Chromosome Location	chr3:133858948-133858949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133858232..133859742-chr3:133862491..133864984,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11711122	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716232	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13059653	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065669	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13067053	0.84[EUR][1000 genomes]
rs13073076	0.83[ASN][1000 genomes]
rs13074310	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075472	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13080318	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13080570	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13096460	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28450327	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28484700	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28622917	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28667241	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28726214	0.84[EUR][1000 genomes]
rs28785783	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28852473	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34678092	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35241315	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35293292	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35338993	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35397189	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35702871	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35750568	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077107	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4241372	0.81[ASN][1000 genomes]
rs4241373	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4241374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4280634	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4305420	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4342102	0.88[EUR][1000 genomes]
rs4345064	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4355279	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4380411	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413311	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4419375	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4426678	0.81[ASN][1000 genomes]
rs4450812	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4507252	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4507253	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4518125	0.81[ASN][1000 genomes]
rs4535222	0.81[ASN][1000 genomes]
rs4546144	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547696	0.88[EUR][1000 genomes]
rs4552343	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4558752	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4640559	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854611	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4854614	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854615	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854809	0.82[ASN][1000 genomes]
rs4854811	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854812	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4854817	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854818	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854820	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854825	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62269301	0.88[EUR][1000 genomes]
rs6439461	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776592	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6777817	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796570	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6802495	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613782	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7632489	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632556	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632691	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7653175	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289460	0.88[EUR][1000 genomes]
rs9790149	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818626	0.81[ASN][1000 genomes]
rs9827105	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831998	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842531	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9843541	0.88[EUR][1000 genomes]
rs9847033	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850689	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9853047	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857486	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857977	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865639	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867748	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869195	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869613	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870910	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9871137	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9877506	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878348	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882875	0.82[EUR][1000 genomes]
rs9884048	0.81[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	nsv965344	chr3:133805086-133862489	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133827600-133862800	Weak transcription	Left Ventricle	heart
2	chr3:133840600-133862800	Weak transcription	Right Ventricle	heart
3	chr3:133840800-133862800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:133842000-133872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:133842600-133862800	Weak transcription	Adipose Nuclei	Adipose
6	chr3:133842600-133870600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:133842800-133872000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:133843000-133871200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:133843000-133872600	Weak transcription	Gastric	stomach
10	chr3:133848200-133862800	Weak transcription	Ovary	ovary
11	chr3:133848400-133866400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:133848400-133867400	Weak transcription	Primary T cells from cord blood	blood
13	chr3:133848600-133865400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:133848600-133867600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:133848600-133872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:133850800-133862800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:133852000-133866000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:133853600-133862800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:133853600-133870600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:133853600-133871000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:133853800-133867400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:133854400-133872400	Weak transcription	NHEK	skin
23	chr3:133855400-133871000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:133856400-133872600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:133857600-133859200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:133858000-133870800	Weak transcription	Fetal Brain Female	brain
27	chr3:133858000-133871800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:133858200-133862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:133858400-133859200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:133858600-133859000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:133858600-133859200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:133858600-133859400	ZNF genes & repeats	Aorta	Aorta
33	chr3:133858800-133859200	ZNF genes & repeats	Esophagus	oesophagus
34	chr3:133858800-133859200	ZNF genes & repeats	Fetal Stomach	stomach
35	chr3:133858800-133859200	ZNF genes & repeats	Lung	lung
36	chr3:133858800-133859200	ZNF genes & repeats	Pancreas	Pancrea
37	chr3:133858800-133859400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:133858800-133859400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:133858800-133862800	Weak transcription	Fetal Muscle Trunk	muscle

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