Variant report

Variant	rs1466759
Chromosome Location	chr12:29303387-29303388
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	GATA3	chr12:29303023-29303443	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:29301843-29303600	PBDE	blood:	n/a	n/a
3	POLR2A	chr12:29301057-29303694	NB4	blood:	n/a	n/a
4	MYC	chr12:29301019-29303692	NB4	blood:	n/a	chr12:29302778-29302787
5	POLR2A	chr12:29301319-29303437	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:29301000-29303723	NB4	blood:	n/a	chr12:29302778-29302787
7	POLR2A	chr12:29301337-29303433	HL-60	blood:	n/a	n/a
8	POLR2A	chr12:29300990-29303986	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:29301106-29303469	HL-60	blood:	n/a	n/a
10	POLR2A	chr12:29301222-29303487	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr12:29301730-29303396	H1-hESC	embryonic stem cell:	n/a	chr12:29302114-29302125 chr12:29302762-29302769 chr12:29302115-29302126 chr12:29302115-29302122 chr12:29302762-29302769 chr12:29302115-29302122 chr12:29302762-29302769 chr12:29302114-29302123 chr12:29301793-29301800 chr12:29302535-29302545 chr12:29302173-29302185 chr12:29302115-29302122 chr12:29302110-29302125 chr12:29302567-29302581 chr12:29302084-29302096 chr12:29302104-29302114
12	POLR2A	chr12:29301171-29303406	GM19099	blood:	n/a	n/a
13	MAX	chr12:29302997-29303444	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000257258	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10843322	1.00[AMR][1000 genomes]
rs11050053	1.00[AMR][1000 genomes]
rs12299859	1.00[AMR][1000 genomes]
rs12302586	1.00[AMR][1000 genomes]
rs12308583	1.00[AMR][1000 genomes]
rs12321950	1.00[AMR][1000 genomes]
rs1826802	1.00[AMR][1000 genomes]
rs2060566	1.00[AMR][1000 genomes]
rs2349968	1.00[AMR][1000 genomes]
rs2349973	0.90[AFR][1000 genomes]
rs61083639	1.00[AMR][1000 genomes]
rs7962268	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963958	0.83[AFR][1000 genomes];1.00[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv819469	chr12:29285461-29303486	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29301000-29303400	Active TSS	Fetal Kidney	kidney
2	chr12:29301000-29303400	Active TSS	Stomach Smooth Muscle	stomach
3	chr12:29301000-29303600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:29301000-29304200	Active TSS	Brain Cingulate Gyrus	brain
5	chr12:29301200-29303400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:29301200-29303400	Active TSS	Colonic Mucosa	Colon
7	chr12:29301200-29303400	Active TSS	Colon Smooth Muscle	Colon
8	chr12:29301200-29303400	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:29301200-29303400	Active TSS	Right Ventricle	heart
10	chr12:29301200-29303600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:29301400-29303800	Active TSS	Brain Anterior Caudate	brain
12	chr12:29301600-29303400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:29301600-29303400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:29301600-29303400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:29301600-29303400	Active TSS	GM12878-XiMat	blood
16	chr12:29301600-29303400	Active TSS	Osteobl	bone
17	chr12:29301600-29303600	Active TSS	NH-A	brain
18	chr12:29302000-29303400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:29302400-29303400	Enhancers	Fetal Brain Male	brain
20	chr12:29302400-29303600	Flanking Active TSS	Dnd41	blood
21	chr12:29302600-29303400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr12:29302600-29303400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr12:29302600-29303400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr12:29302600-29303400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:29302600-29303400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:29302600-29303600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:29302600-29304200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:29302600-29304600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:29302600-29306800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:29302800-29303400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr12:29302800-29303400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr12:29302800-29303600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:29302800-29303800	Flanking Active TSS	HUVEC	blood vessel
34	chr12:29302800-29304000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:29302800-29304800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr12:29303000-29303400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr12:29303000-29303400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr12:29303000-29303400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:29303000-29303400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:29303000-29303400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:29303000-29303400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:29303000-29303400	Active TSS	Brain Hippocampus Middle	brain
43	chr12:29303000-29303400	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr12:29303000-29303400	Flanking Active TSS	Fetal Brain Female	brain
45	chr12:29303000-29303400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr12:29303000-29303400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr12:29303000-29303400	Enhancers	Stomach Mucosa	stomach
48	chr12:29303000-29303400	Flanking Active TSS	Spleen	Spleen
49	chr12:29303000-29303600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
50	chr12:29303000-29303600	Flanking Active TSS	Primary T cells from cord blood	blood

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