Variant report

Variant	rs1564408
Chromosome Location	chr3:138071329-138071330
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138065032..138067985-chr3:138070541..138072955,3	MCF-7	breast:
2	chr3:138066416..138068564-chr3:138071079..138073147,2	K562	blood:
3	chr3:138065895..138067916-chr3:138070047..138072579,2	K562	blood:
4	chr3:138069326..138072318-chr3:138105183..138106708,2	K562	blood:

Variant related genes	Relation type
ENSG00000158186	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002766	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1092338	0.81[ASN][1000 genomes]
rs11710280	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11713141	0.88[EUR][1000 genomes]
rs1199330	0.81[ASN][1000 genomes]
rs1199331	0.83[EUR][1000 genomes]
rs1199337	0.81[ASN][1000 genomes]
rs1199338	0.82[ASN][1000 genomes]
rs12107581	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490350	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13324341	0.84[ASN][1000 genomes]
rs1564407	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678440	0.81[ASN][1000 genomes]
rs1679147	0.88[EUR][1000 genomes]
rs1720819	0.81[ASN][1000 genomes]
rs185244	0.81[ASN][1000 genomes]
rs1904349	0.83[ASN][1000 genomes]
rs2054468	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2061936	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169973	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293252	0.80[EUR][1000 genomes]
rs35219044	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755751	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773752	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773758	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3773759	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816730	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678260	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678261	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678407	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678408	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4678409	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678410	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4678411	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678412	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678415	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4678417	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6439804	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6439805	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6439806	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6439807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67559768	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6766859	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769236	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6769261	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782181	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782449	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6784989	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6789235	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6790398	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802211	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs730158	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731632	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751357	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615658	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626388	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626424	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637666	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7642400	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9289559	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs940233	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825697	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9834911	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9845672	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846198	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846223	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854465	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9855722	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068400-138083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:138068600-138071800	Enhancers	Placenta	Placenta
3	chr3:138068600-138084600	Weak transcription	Gastric	stomach
4	chr3:138068800-138075800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:138068800-138076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:138069000-138073600	Weak transcription	Fetal Stomach	stomach
8	chr3:138069000-138076000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:138069000-138077800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:138069200-138074000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:138069200-138075600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:138069200-138088200	Weak transcription	Fetal Lung	lung
13	chr3:138069400-138071800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:138069400-138071800	Enhancers	Fetal Muscle Leg	muscle
15	chr3:138069400-138073600	Enhancers	Psoas Muscle	Psoas
16	chr3:138069400-138074000	Weak transcription	Fetal Brain Female	brain
17	chr3:138069400-138075600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:138069400-138078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:138069400-138080600	Weak transcription	NHLF	lung
20	chr3:138069600-138071600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:138070000-138075400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
23	chr3:138070200-138072800	Weak transcription	Osteobl	bone
24	chr3:138070200-138073400	Enhancers	Adipose Nuclei	Adipose
25	chr3:138070200-138073400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:138070200-138074000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:138070200-138086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:138070600-138071600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:138070600-138073400	Enhancers	Right Ventricle	heart
30	chr3:138070800-138071600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:138070800-138071800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:138070800-138071800	Enhancers	Left Ventricle	heart
33	chr3:138070800-138075000	Weak transcription	Brain Angular Gyrus	brain
34	chr3:138070800-138075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:138070800-138076800	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:138071000-138071600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:138071000-138071800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:138071000-138074000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:138071000-138074200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:138071000-138074200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:138071000-138074400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:138071000-138075600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:138071000-138085600	Weak transcription	Brain Germinal Matrix	brain
44	chr3:138071200-138072200	Weak transcription	Right Atrium	heart
45	chr3:138071200-138072200	Genic enhancers	HSMMtube	muscle
46	chr3:138071200-138072400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:138071200-138072800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:138071200-138073200	Enhancers	Fetal Heart	heart
49	chr3:138071200-138073600	Genic enhancers	HSMM	muscle
50	chr3:138071200-138074000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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