Variant report

Variant	rs654219
Chromosome Location	chr3:101586400-101586401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101580233..101583305-chr3:101583539..101587292,4	MCF-7	breast:
2	chr3:101566766..101570360-chr3:101584530..101589455,9	K562	blood:
3	chr3:101579733..101582231-chr3:101586214..101587779,2	K562	blood:
4	chr3:101586222..101589351-chr3:101592319..101595732,4	K562	blood:
5	chr3:101586222..101589351-chr3:101592520..101595732,3	K562	blood:
6	chr3:101566766..101570360-chr3:101585005..101589455,7	K562	blood:

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:19)

rs_ID	r²[population]
rs14134	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2925332	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925333	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926539	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587555	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs592332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599849	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601225	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs618901	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622122	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs665374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677011	0.82[ASN][1000 genomes]
rs678354	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs680508	0.82[ASN][1000 genomes]
rs681573	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS 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	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	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
5	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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101576400-101586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:101576400-101586800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:101579200-101586400	Weak transcription	Fetal Kidney	kidney
5	chr3:101579200-101586400	Weak transcription	K562	blood
6	chr3:101579400-101586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:101579400-101586400	Weak transcription	Small Intestine	intestine
8	chr3:101579400-101586600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:101579400-101587200	Weak transcription	NHEK	skin
10	chr3:101579400-101587400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:101579400-101587600	Weak transcription	Aorta	Aorta
12	chr3:101579400-101587600	Weak transcription	Gastric	stomach
13	chr3:101579400-101587600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:101579400-101587800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:101579400-101588600	Weak transcription	Esophagus	oesophagus
16	chr3:101580000-101587400	Weak transcription	Fetal Lung	lung
17	chr3:101580400-101587600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:101580800-101587400	Weak transcription	HMEC	breast
19	chr3:101580800-101587600	Weak transcription	Placenta	Placenta
20	chr3:101580800-101588600	Weak transcription	NHDF-Ad	bronchial
21	chr3:101581000-101586400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:101581200-101586400	Weak transcription	Pancreas	Pancrea
23	chr3:101581200-101587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:101581200-101587400	Weak transcription	Primary B cells from cord blood	blood
25	chr3:101581200-101587600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:101581400-101586400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:101581400-101586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:101581400-101586400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:101581400-101586600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:101581400-101587200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:101581400-101587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:101581400-101587600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:101581600-101587200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:101581600-101587400	Weak transcription	Adipose Nuclei	Adipose
35	chr3:101581600-101587600	Weak transcription	GM12878-XiMat	blood
36	chr3:101581800-101587000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:101581800-101587200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:101582000-101586600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:101582000-101587000	Weak transcription	Left Ventricle	heart
40	chr3:101582000-101587200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:101582000-101587600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:101583200-101587400	Enhancers	Liver	Liver
43	chr3:101583400-101588800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:101583400-101598000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:101584400-101587000	Enhancers	A549	lung
46	chr3:101584600-101586400	Weak transcription	Osteobl	bone
47	chr3:101584600-101588800	Enhancers	Fetal Intestine Large	intestine
48	chr3:101585000-101586400	Weak transcription	NH-A	brain
49	chr3:101585200-101586400	Weak transcription	Fetal Intestine Small	intestine
50	chr3:101585200-101586400	Weak transcription	HepG2	liver

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