Variant report

Variant	rs13427080
Chromosome Location	chr2:127865753-127865754
allele	C/T
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	POLR2A	chr2:127862777-127866023	IMR90	lung:	n/a	n/a
2	MXI1	chr2:127862712-127865788	SK-N-SH	brain:	n/a	chr2:127864072-127864081 chr2:127864371-127864380
3	GATA2	chr2:127864991-127865860	SH-SY5Y	brain:	n/a	chr2:127865545-127865552

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127865657..127869658-chr2:127871080..127873352,3	K562	blood:

Variant related genes	Relation type
BIN1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10198772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204965	1.00[ASN][1000 genomes]
rs11674215	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683933	0.94[EUR][1000 genomes]
rs11688714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11688763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11692858	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11695202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13416395	1.00[ASN][1000 genomes]
rs13417002	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417187	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419729	1.00[ASN][1000 genomes]
rs3845673	1.00[ASN][1000 genomes]
rs56772251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56827597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56853185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959054	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959055	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72959066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72959067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749009	0.97[EUR][1000 genomes]
rs7575579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7583814	0.87[ASN][1000 genomes]
rs7584040	0.87[ASN][1000 genomes]
rs7600660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9653201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9653202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9653203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9653206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv1005149	chr2:127841930-127880106	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127862800-127865800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:127863000-127865800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:127863000-127865800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:127863000-127866200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:127863200-127865800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:127863400-127865800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:127863400-127866000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:127863800-127865800	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr2:127864600-127865800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr2:127865000-127865800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:127865000-127865800	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr2:127865000-127866000	Flanking Active TSS	Fetal Muscle Trunk	muscle
13	chr2:127865200-127865800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:127865200-127865800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:127865200-127865800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:127865200-127865800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr2:127865200-127865800	Flanking Active TSS	HSMM	muscle
18	chr2:127865200-127865800	Flanking Active TSS	NHEK	skin
19	chr2:127865200-127866000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:127865200-127866000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr2:127865200-127866000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr2:127865200-127866000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:127865200-127866000	Flanking Bivalent TSS/Enh	HepG2	liver
24	chr2:127865400-127865800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:127865400-127865800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:127865400-127865800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr2:127865400-127865800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr2:127865400-127865800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
29	chr2:127865400-127865800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:127865400-127865800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr2:127865400-127865800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:127865400-127865800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:127865400-127865800	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr2:127865400-127865800	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr2:127865400-127865800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:127865400-127865800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr2:127865400-127865800	Enhancers	Small Intestine	intestine
38	chr2:127865400-127865800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr2:127865400-127865800	Flanking Active TSS	GM12878-XiMat	blood
40	chr2:127865400-127866000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:127865400-127866000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr2:127865400-127866000	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr2:127865400-127866000	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr2:127865400-127866000	Enhancers	Spleen	Spleen
45	chr2:127865400-127866200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:127865400-127866200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr2:127865400-127866200	Enhancers	Left Ventricle	heart
48	chr2:127865600-127865800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:127865600-127865800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:127865600-127865800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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