Variant report

Variant	rs72940009
Chromosome Location	chr3:112257869-112257870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112257078..112259281-chr3:112279236..112282506,3	MCF-7	breast:
2	chr3:112257611..112259171-chr3:112300442..112301943,2	K562	blood:

Variant related genes	Relation type
ENSG00000138459	Chromatin interaction
ENSG00000144848	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13070342	0.94[AFR][1000 genomes]
rs57937078	1.00[AMR][1000 genomes]
rs59090018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938420	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938422	1.00[AMR][1000 genomes]
rs72938432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938438	1.00[AMR][1000 genomes]
rs72938454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942068	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942074	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942089	1.00[AMR][1000 genomes]
rs72943904	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription 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	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
8	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
9	chr3:112244400-112278200	Weak transcription	K562	blood
10	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
11	chr3:112244600-112264800	Weak transcription	NHEK	skin
12	chr3:112245200-112263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:112245400-112262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:112245600-112258000	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:112245600-112258200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:112245800-112261400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:112245800-112261800	Strong transcription	Dnd41	blood
19	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:112246200-112264600	Weak transcription	Fetal Heart	heart
21	chr3:112247000-112267800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:112247200-112261000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:112247800-112265800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:112248000-112264800	Weak transcription	Ovary	ovary
26	chr3:112248200-112264200	Weak transcription	Fetal Brain Female	brain
27	chr3:112248200-112264800	Weak transcription	HepG2	liver
28	chr3:112248400-112259600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:112248400-112265600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:112248400-112266200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:112248800-112265000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:112249000-112263600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:112249000-112264800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:112249000-112265400	Weak transcription	Right Ventricle	heart
36	chr3:112249200-112265000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:112249200-112265800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:112249200-112269800	Weak transcription	Psoas Muscle	Psoas
39	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
40	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
41	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
43	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
44	chr3:112249200-112279600	Weak transcription	Gastric	stomach
45	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:112249400-112264600	Weak transcription	Thymus	Thymus
47	chr3:112249400-112270000	Weak transcription	Fetal Intestine Small	intestine
48	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:112249400-112279600	Weak transcription	Lung	lung
50	chr3:112249600-112264600	Weak transcription	Brain Hippocampus Middle	brain

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