Variant report

Variant	rs2279759
Chromosome Location	chr12:106694988-106694989
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	MAFK	chr12:106694568-106695910	K562	blood:	n/a	n/a
2	EBF1	chr12:106694967-106696819	GM12878	blood:	n/a	chr12:106695605-106695616
3	MXI1	chr12:106694917-106697676	IMR90	lung:	n/a	n/a
4	GATA1	chr12:106694718-106696081	K562	blood:	n/a	n/a
5	GATA1	chr12:106694402-106696053	PBDE	blood:	n/a	chr12:106694528-106694535 chr12:106694528-106694535 chr12:106694521-106694542 chr12:106694527-106694537 chr12:106694528-106694535
6	MAZ	chr12:106694985-106697657	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:106693946..106698218-chr12:106750404..106754111,7	MCF-7	breast:
2	chr12:106639346..106644112-chr12:106694122..106698214,13	MCF-7	breast:
3	chr12:106693434..106696954-chr12:106697519..106701215,4	MCF-7	breast:
4	chr12:106694726..106698780-chr12:106749876..106753760,9	K562	blood:
5	chr12:106640063..106644049-chr12:106694395..106698756,11	MCF-7	breast:

Variant related genes	Relation type
TCP11L2	TF binding region
ENSG00000136026	Chromatin interaction
ENSG00000166046	Chromatin interaction
ENSG00000013503	Chromatin interaction
ENSG00000258355	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10861572	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861574	1.00[ASN][1000 genomes]
rs10861575	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs11112931	0.95[ASN][1000 genomes]
rs12831519	0.83[CEU][hapmap]
rs1532587	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs17217845	0.83[CEU][hapmap]
rs2077730	0.89[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2249837	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2250108	0.89[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2250705	0.98[ASN][1000 genomes]
rs2250708	0.97[ASN][1000 genomes]
rs2250709	0.99[ASN][1000 genomes]
rs2250713	0.98[ASN][1000 genomes]
rs2250936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2264757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2264762	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2264814	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2264815	0.89[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2264816	0.86[ASN][1000 genomes]
rs2465356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35816179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36139467	0.99[ASN][1000 genomes]
rs7314289	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs904614	0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794382	chr12:106679812-106699151	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279759	C12orf23	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106680000-106695200	Weak transcription	Right Atrium	heart
2	chr12:106685800-106695200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:106685800-106695200	Weak transcription	Fetal Lung	lung
4	chr12:106689000-106695800	Weak transcription	Lung	lung
5	chr12:106690200-106695400	Weak transcription	NHLF	lung
6	chr12:106690600-106695000	Weak transcription	NH-A	brain
7	chr12:106690600-106695200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:106690600-106695400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:106690800-106695000	Weak transcription	HMEC	breast
10	chr12:106690800-106695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:106690800-106695400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:106691800-106695000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:106691800-106695000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:106691800-106695000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:106691800-106695000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:106691800-106695200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:106691800-106695200	Weak transcription	Esophagus	oesophagus
18	chr12:106691800-106695200	Weak transcription	GM12878-XiMat	blood
19	chr12:106691800-106695400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:106692000-106695000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:106692200-106695200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:106693000-106695200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:106693000-106695200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:106693000-106695200	Enhancers	HepG2	liver
25	chr12:106693000-106695400	Enhancers	Left Ventricle	heart
26	chr12:106693000-106695400	Enhancers	K562	blood
27	chr12:106693200-106695200	Weak transcription	Fetal Intestine Small	intestine
28	chr12:106693200-106695400	Weak transcription	Colonic Mucosa	Colon
29	chr12:106693400-106695000	Weak transcription	Fetal Intestine Large	intestine
30	chr12:106693400-106695400	Weak transcription	Psoas Muscle	Psoas
31	chr12:106693400-106695800	Weak transcription	Gastric	stomach
32	chr12:106693400-106695800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:106693600-106695200	Enhancers	HSMMtube	muscle
34	chr12:106694000-106695200	Weak transcription	Right Ventricle	heart
35	chr12:106694000-106695400	Enhancers	Brain Hippocampus Middle	brain
36	chr12:106694200-106695200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:106694200-106695200	Enhancers	Stomach Mucosa	stomach
38	chr12:106694200-106695400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:106694200-106695400	Weak transcription	Placenta	Placenta
40	chr12:106694200-106695400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:106694400-106695000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:106694400-106695000	Enhancers	Hela-S3	cervix
43	chr12:106694400-106695200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:106694400-106695200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:106694400-106695200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:106694400-106695400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:106694400-106695600	Enhancers	Primary hematopoietic stem cells	blood
48	chr12:106694400-106695800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:106694600-106695000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr12:106694600-106695000	Enhancers	Rectal Mucosa Donor 29	rectum

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