Variant report

Variant	rs2470939
Chromosome Location	chr7:104581510-104581511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:104581168-104582454	GM12892	blood:	n/a	n/a
2	TAF1	chr7:104581275-104581527	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:104581256-104581716	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:104581220-104581613	GM12891	blood:	n/a	n/a
5	TAF1	chr7:104581203-104581524	GM12891	blood:	n/a	n/a
6	PML	chr7:104581128-104581692	GM12878	blood:	n/a	n/a
7	HEY1	chr7:104581260-104581518	K562	blood:	n/a	n/a
8	SP1	chr7:104581117-104581533	GM12878	blood:	n/a	n/a
9	SP1	chr7:104581083-104581583	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:104581218-104582809	GM19099	blood:	n/a	n/a
11	TAF1	chr7:104581232-104581557	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:104581304-104581511	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFYB	chr7:104581006-104581554	K562	blood:	n/a	chr7:104581319-104581334
14	POLR2A	chr7:104581204-104581645	GM12891	blood:	n/a	n/a
15	POLR2A	chr7:104581253-104582366	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:104581159-104582883	GM12878	blood:	n/a	n/a
17	POU2F2	chr7:104581186-104582008	GM12891	blood:	n/a	n/a
18	POLR2A	chr7:104581223-104582762	GM19193	blood:	n/a	n/a
19	POU2F2	chr7:104581253-104582137	GM12891	blood:	n/a	n/a
20	POLR2A	chr7:104581226-104581614	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:104581105-104581775	GM12891	blood:	n/a	n/a
22	POLR2A	chr7:104581203-104582272	GM12891	blood:	n/a	n/a
23	POU2F2	chr7:104581289-104581574	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:104581219-104581598	GM18505	blood:	n/a	n/a
25	POLR2A	chr7:104581217-104581602	GM15510	blood:	n/a	n/a
26	YY1	chr7:104581260-104581547	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:104581261-104582367	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:104581060-104582884	GM12892	blood:	n/a	n/a
29	POLR2A	chr7:104581109-104582754	GM12891	blood:	n/a	n/a
30	RUNX3	chr7:104581271-104581720	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:104581227-104581598	NB4	blood:	n/a	n/a
32	POLR2A	chr7:104581124-104581724	GM12892	blood:	n/a	n/a
33	TAF1	chr7:104581246-104581545	GM12891	blood:	n/a	n/a
34	RUNX3	chr7:104581378-104582079	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:104581218-104582352	GM18951	blood:	n/a	n/a
36	TCF3	chr7:104581196-104581546	GM12878	blood:	n/a	n/a
37	FOXM1	chr7:104581162-104581825	GM12878	blood:	n/a	n/a
38	TCF3	chr7:104581279-104581518	GM12878	blood:	n/a	n/a
39	POLR2A	chr7:104581256-104582805	GM12878	blood:	n/a	n/a
40	CTCF	chr7:104581452-104581573	Spleen_OC	spleen:	n/a	n/a
41	POLR2A	chr7:104581219-104581659	GM18526	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104579927..104586214-chr7:104652770..104656015,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237513	TF binding region
ENSG00000228393	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000239569	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10266287	0.88[ASN][1000 genomes]
rs10953460	0.89[ASN][1000 genomes]
rs2430484	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430486	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470938	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470940	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470941	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470942	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470943	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470944	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470945	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470947	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470948	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470949	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470950	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727614	0.92[ASN][1000 genomes]
rs6955349	0.92[ASN][1000 genomes]
rs6965384	0.88[ASN][1000 genomes]
rs7776707	0.88[ASN][1000 genomes]
rs916705	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104569800-104584000	Weak transcription	Esophagus	oesophagus
2	chr7:104573800-104583200	Weak transcription	Fetal Heart	heart
3	chr7:104574400-104582000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:104575200-104581600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:104575200-104581800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:104575400-104582000	Weak transcription	Stomach Mucosa	stomach
7	chr7:104580000-104585400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:104580200-104582000	Weak transcription	HepG2	liver
9	chr7:104580400-104584000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:104580400-104584000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:104580400-104584000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:104580400-104584200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:104580400-104584200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:104580600-104582800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:104580600-104583800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:104580800-104582600	ZNF genes & repeats	Fetal Thymus	thymus
17	chr7:104581000-104582000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:104581000-104582000	Weak transcription	Spleen	Spleen
19	chr7:104581000-104582600	Weak transcription	Pancreas	Pancrea
20	chr7:104581000-104584000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:104581000-104584400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr7:104581000-104585600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:104581000-104586800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:104581200-104581600	Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr7:104581200-104581600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr7:104581200-104581800	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr7:104581200-104581800	Active TSS	Primary T cells from cord blood	blood
28	chr7:104581200-104581800	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr7:104581200-104581800	Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr7:104581200-104581800	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr7:104581200-104582000	Active TSS	Primary B cells from cord blood	blood
32	chr7:104581200-104582000	Active TSS	Primary B cells from peripheral blood	blood
33	chr7:104581200-104582000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr7:104581200-104582000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:104581200-104582400	Active TSS	Fetal Kidney	kidney
36	chr7:104581200-104582600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr7:104581200-104582600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:104581400-104581600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:104581400-104581600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:104581400-104581600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:104581400-104581800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr7:104581400-104581800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr7:104581400-104581800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr7:104581400-104581800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:104581400-104581800	Active TSS	GM12878-XiMat	blood
46	chr7:104581400-104582000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr7:104581400-104582000	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr7:104581400-104582000	Active TSS	Duodenum Mucosa	Duodenum
49	chr7:104581400-104582200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:104581400-104582400	Active TSS	Stomach Smooth Muscle	stomach

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