Variant report

Variant	rs72931150
Chromosome Location	chr2:39665732-39665733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr2:39665060-39665967	MCF10A-Er-Src	breast:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
2	POLR2A	chr2:39663734-39666027	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr2:39662210-39666175	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:39663814-39665976	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr2:39665088-39666012	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr2:39665056-39665798	K562	blood:	n/a	chr2:39665749-39665759
7	NFIC	chr2:39664212-39665829	HepG2	liver:	n/a	chr2:39665114-39665142
8	STAT3	chr2:39665090-39666138	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr2:39664979-39665773	MCF10A-Er-Src	breast:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274

No.	Distal block	Cell Line	Cell type
1	chr17:43236605..43238756-chr2:39663829..39665960,2	MCF-7	breast:
2	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
3	chr2:39664730..39667183-chr2:39678037..39681016,2	MCF-7	breast:

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000224505	Chromatin interaction
ENSG00000168517	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12105018	0.91[AMR][1000 genomes]
rs57107827	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs57164521	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58019817	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706951	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6722096	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6725496	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6725704	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6759388	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72914206	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72925278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72925283	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72925290	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927103	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927107	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927108	1.00[AMR][1000 genomes]
rs72927110	1.00[AMR][1000 genomes]
rs72927119	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72927123	0.85[AMR][1000 genomes]
rs72927143	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72929164	0.91[AMR][1000 genomes]
rs72929184	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931129	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931131	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931135	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931145	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931172	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7566368	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7581123	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7592925	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7609233	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:39661800-39667000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:39661800-39667000	Active TSS	Aorta	Aorta
4	chr2:39662000-39665800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:39662000-39666000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr2:39662000-39666200	Active TSS	Ovary	ovary
7	chr2:39662400-39666000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:39662600-39666000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:39662600-39666000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:39663000-39665800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:39663000-39666000	Active TSS	Colon Smooth Muscle	Colon
12	chr2:39663600-39666000	Active TSS	Duodenum Mucosa	Duodenum
13	chr2:39664600-39665800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr2:39664600-39665800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:39664800-39665800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:39664800-39667000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:39665000-39665800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:39665000-39666000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr2:39665000-39666200	Flanking Active TSS	Osteobl	bone
20	chr2:39665000-39666600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:39665000-39667000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr2:39665200-39665800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:39665200-39665800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:39665200-39665800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:39665200-39665800	Flanking Active TSS	Fetal Lung	lung
26	chr2:39665200-39665800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:39665200-39666200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:39665200-39666200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:39665200-39666800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:39665200-39667000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:39665200-39667000	Weak transcription	Small Intestine	intestine
32	chr2:39665200-39667000	Flanking Active TSS	NHLF	lung
33	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:39665400-39665800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr2:39665400-39665800	Flanking Active TSS	Liver	Liver
36	chr2:39665400-39665800	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr2:39665400-39665800	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr2:39665400-39665800	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:39665400-39665800	Flanking Active TSS	A549	lung
40	chr2:39665400-39666200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:39665400-39666600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:39665400-39666600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:39665400-39667000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:39665400-39667200	Enhancers	Stomach Mucosa	stomach
45	chr2:39665400-39667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:39665400-39667800	Weak transcription	Esophagus	oesophagus
47	chr2:39665600-39665800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:39665600-39665800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr2:39665600-39665800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:39665600-39665800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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