Variant report

Variant	rs71446055
Chromosome Location	chr2:32390054-32390055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:32389013-32390138	K562	blood:	n/a	n/a
2	MYC	chr2:32389830-32390281	MCF10A-Er-Src	breast:	n/a	chr2:32390094-32390105
3	MYBL2	chr2:32389953-32391497	HepG2	liver:	n/a	n/a
4	GTF3C2	chr2:32389913-32391268	K562	blood:	n/a	n/a
5	POLR2A	chr2:32389104-32392168	K562	blood:	n/a	n/a
6	POLR2A	chr2:32388937-32390346	K562	blood:	n/a	n/a
7	POLR2A	chr2:32389695-32390056	SK-N-SH	brain:	n/a	n/a
8	GTF3C2	chr2:32389942-32391096	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:32389843-32391924	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr2:32389076-32390109	K562	blood:	n/a	n/a
11	POLR2A	chr2:32390000-32390062	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:32389361-32390139	K562	blood:	n/a	n/a
13	POLR2A	chr2:32389652-32391597	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr2:32389471-32390067	PBDE	blood:	n/a	n/a
15	MYC	chr2:32390010-32391167	MCF10A-Er-Src	breast:	n/a	chr2:32390094-32390105
16	IRF1	chr2:32389733-32390169	K562	blood:	n/a	n/a
17	IRF1	chr2:32389771-32390160	K562	blood:	n/a	n/a
18	MXI1	chr2:32389629-32391587	IMR90	lung:	n/a	n/a
19	POLR2A	chr2:32389831-32391818	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr2:32389755-32390189	IMR90	lung:	n/a	n/a
21	MXI1	chr2:32389527-32392277	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr2:32389520-32392007	K562	blood:	n/a	n/a
23	HEY1	chr2:32388941-32391958	K562	blood:	n/a	chr2:32391190-32391205
24	MXI1	chr2:32389721-32390100	K562	blood:	n/a	n/a
25	MYC	chr2:32389476-32390091	K562	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32263820..32266854-chr2:32389080..32393861,5	MCF-7	breast:
2	chr2:32388440..32390986-chr2:32579691..32583834,6	K562	blood:
3	chr2:32287339..32289467-chr2:32389793..32392170,2	MCF-7	breast:
4	chr2:32387435..32390295-chr2:32587080..32590116,3	K562	blood:
5	chr2:32390024..32393805-chr2:32579476..32583220,6	K562	blood:
6	chr2:32295719..32297694-chr2:32389118..32390763,2	K562	blood:
7	chr2:32263395..32265602-chr2:32389530..32391691,2	MCF-7	breast:
8	chr2:32264868..32267001-chr2:32389298..32391324,2	K562	blood:
9	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
10	chr2:32107600..32109917-chr2:32388289..32390102,3	K562	blood:
11	chr2:32389583..32392652-chr2:32503120..32506003,3	K562	blood:
12	chr2:32234641..32236375-chr2:32389314..32391737,5	MCF-7	breast:
13	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
14	chr2:32287157..32290220-chr2:32389830..32392599,3	MCF-7	breast:
15	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
16	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:
17	chr2:32388347..32391315-chr6:27100140..27102328,2	MCF-7	breast:
18	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
19	chr2:32112402..32115115-chr2:32387877..32390821,4	K562	blood:
20	chr2:32264101..32266985-chr2:32387828..32391332,6	K562	blood:

No data

Variant related genes	Relation type
SLC30A6	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000119820	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000021574	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11887458	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11895183	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11895623	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13006302	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13029716	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145038	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35245684	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35560333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35653492	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3851309	0.86[ASN][1000 genomes]
rs58980266	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60386495	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60906113	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6543653	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719805	0.85[ASN][1000 genomes]
rs6757121	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71446044	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71446045	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71446054	0.97[AFR][1000 genomes]
rs71446056	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72493393	0.80[AFR][1000 genomes]
rs72863973	0.85[ASN][1000 genomes]
rs72863977	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7580118	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32331600-32390200	Weak transcription	Gastric	stomach
2	chr2:32331600-32390200	Weak transcription	Pancreas	Pancrea
3	chr2:32354600-32390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:32355000-32390200	Weak transcription	Small Intestine	intestine
5	chr2:32360000-32390200	Weak transcription	Ovary	ovary
6	chr2:32371000-32390200	Weak transcription	Left Ventricle	heart
7	chr2:32371000-32390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:32379400-32390200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:32381800-32390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:32383600-32390200	Weak transcription	Fetal Thymus	thymus
11	chr2:32383800-32390200	Weak transcription	HSMMtube	muscle
12	chr2:32389000-32390200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr2:32389200-32392000	Active TSS	NHLF	lung
14	chr2:32389400-32390400	Flanking Active TSS	Dnd41	blood
15	chr2:32389400-32391600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:32389400-32391800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:32389400-32391800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:32389400-32392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:32389400-32392600	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:32389400-32392600	Active TSS	K562	blood
21	chr2:32389600-32390200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:32389600-32390200	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:32389600-32390200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:32389600-32390200	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:32389600-32390200	Enhancers	Colon Smooth Muscle	Colon
26	chr2:32389600-32390200	Enhancers	Fetal Heart	heart
27	chr2:32389600-32390200	Flanking Active TSS	Osteobl	bone
28	chr2:32389600-32391600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:32389600-32391600	Active TSS	A549	lung
30	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:32389600-32391800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:32389600-32392200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr2:32389600-32392200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:32389600-32392200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:32389800-32390200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:32389800-32390200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr2:32389800-32390200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:32389800-32390200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:32389800-32390200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:32389800-32390200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:32389800-32390200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr2:32389800-32390200	Active TSS	Thymus	Thymus
44	chr2:32389800-32390200	Flanking Active TSS	HUVEC	blood vessel
45	chr2:32389800-32391200	Active TSS	Primary hematopoietic stem cells	blood
46	chr2:32389800-32391400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:32389800-32391400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:32389800-32391400	Active TSS	Fetal Kidney	kidney
49	chr2:32389800-32391400	Active TSS	HMEC	breast
50	chr2:32389800-32391600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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