Variant report

Variant	rs1672396
Chromosome Location	chr3:101644145-101644146
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	chr3:101642851..101646450-chr3:101646744..101649155,3	MCF-7	breast:
2	chr3:101566961..101569726-chr3:101642997..101646954,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1464038	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1626282	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1672395	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672397	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707607	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707608	0.88[AFR][1000 genomes]
rs1707609	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707611	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2942716	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951443	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951446	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34601543	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34922383	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35546667	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67778216	0.80[ASN][1000 genomes]
rs9817370	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9830797	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9869235	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869241	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869399	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9869515	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101642600-101644600	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr3:101642800-101644600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:101643000-101644400	Enhancers	Primary T cells fromperipheralblood	blood
4	chr3:101643000-101644800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:101643000-101644800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:101643200-101644200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:101643200-101644400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:101643200-101644400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:101643200-101644400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:101643200-101644400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:101643200-101644600	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:101643200-101644800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:101643200-101644800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr3:101643200-101644800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:101643200-101645000	Enhancers	Stomach Mucosa	stomach
16	chr3:101643200-101645800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:101643200-101646000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:101643200-101646000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:101643200-101646200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:101643400-101644400	Enhancers	Esophagus	oesophagus
21	chr3:101643400-101644600	Enhancers	Primary T cells from cord blood	blood
22	chr3:101643400-101646200	Enhancers	NHEK	skin
23	chr3:101643400-101646800	Enhancers	HMEC	breast
24	chr3:101643600-101644200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:101643600-101644600	Enhancers	K562	blood
26	chr3:101643600-101644600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:101643600-101645600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:101643600-101646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:101643600-101646200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:101643600-101649200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:101643600-101654000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:101643800-101644200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:101643800-101644400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:101643800-101644400	Enhancers	A549	lung
35	chr3:101643800-101644800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:101643800-101645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:101643800-101646000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:101643800-101658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:101644000-101644400	Weak transcription	Osteobl	bone
40	chr3:101644000-101645400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:101644000-101645400	Weak transcription	HSMMtube	muscle
42	chr3:101644000-101654400	Weak transcription	Primary B cells from cord blood	blood

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