Variant report

Variant	rs11063079
Chromosome Location	chr12:4429569-4429570
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	MTA3	chr12:4429385-4430042	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:4429480-4431095	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:4429526-4430997	GM12892	blood:	n/a	n/a
4	MAX	chr12:4429535-4430823	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:4429531-4430717	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:4429550-4431036	GM12892	blood:	n/a	n/a
7	MXI1	chr12:4429314-4431278	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:4429521-4429575	HUVEC	blood vessel:	n/a	n/a
9	TCF7L2	chr12:4429551-4430353	PANC-1	pancreas:	n/a	n/a
10	MAZ	chr12:4429477-4430847	IMR90	lung:	n/a	n/a
11	MAX	chr12:4429465-4430748	ECC-1	luminal epithelium:	n/a	n/a
12	SP1	chr12:4429494-4430603	H1-hESC	embryonic stem cell:	n/a	chr12:4430227-4430240 chr12:4430186-4430207 chr12:4430230-4430242 chr12:4430161-4430170 chr12:4430261-4430270 chr12:4430260-4430272 chr12:4430230-4430242 chr12:4430232-4430241 chr12:4430159-4430171 chr12:4430159-4430171 chr12:4430231-4430240 chr12:4430262-4430271
13	RUNX3	chr12:4429560-4430842	GM12878	blood:	n/a	chr12:4430074-4430083 chr12:4430065-4430082
14	MTA3	chr12:4429356-4431016	GM12878	blood:	n/a	n/a
15	RCOR1	chr12:4429492-4431232	IMR90	lung:	n/a	n/a
16	POLR2A	chr12:4429469-4430916	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:4429485-4430800	HUVEC	blood vessel:	n/a	n/a
18	GTF2F1	chr12:4429556-4430761	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:4429503-4430865	Hela-S3	cervix:	n/a	n/a
20	MAX	chr12:4429444-4430842	A549	lung:	n/a	n/a
21	PML	chr12:4429403-4430859	GM12878	blood:	n/a	n/a
22	MAX	chr12:4429555-4430744	A549	lung:	n/a	n/a
23	REST	chr12:4429536-4431186	H1-neurons	neurons:	n/a	chr12:4430546-4430559 chr12:4430019-4430039
24	POLR2A	chr12:4429446-4431096	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:4429493-4431050	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:4429552-4430218	GM12892	blood:	n/a	n/a
27	MXI1	chr12:4429470-4431203	IMR90	lung:	n/a	n/a
28	BCL3	chr12:4429528-4430216	A549	lung:	n/a	n/a
29	POLR2A	chr12:4429409-4430941	H1-hESC	embryonic stem cell:	n/a	n/a
30	RELA	chr12:4429555-4430921	GM19099	blood:	n/a	n/a
31	HCFC1	chr12:4429523-4430958	Hela-S3	cervix:	n/a	n/a
32	REST	chr12:4429559-4430222	A549	lung:	n/a	chr12:4430019-4430039
33	SP1	chr12:4429535-4430211	H1-hESC	embryonic stem cell:	n/a	chr12:4430186-4430207 chr12:4430161-4430170 chr12:4430159-4430171 chr12:4430159-4430171
34	TCF12	chr12:4429437-4430848	A549	lung:	n/a	chr12:4430174-4430181 chr12:4430655-4430665
35	E2F6	chr12:4429551-4430664	A549	lung:	n/a	chr12:4430160-4430169 chr12:4430214-4430223
36	POLR2A	chr12:4429559-4430606	H1-hESC	embryonic stem cell:	n/a	n/a
37	RELA	chr12:4429555-4430862	GM10847	blood:	n/a	n/a
38	POLR2A	chr12:4429558-4430981	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:4426548..4433577-chr12:4433933..4442534,18	MCF-7	breast:
2	chr12:4423393..4425090-chr12:4428097..4430311,2	MCF-7	breast:
3	chr1:45196411..45196952-chr12:4429178..4430143,2	Hela-S3	cervix:

Variant related genes	Relation type
C12orf5	TF binding region
ENSG00000213970	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7953609	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4413200-4429800	Weak transcription	Spleen	Spleen
2	chr12:4415200-4429600	Weak transcription	Aorta	Aorta
3	chr12:4417000-4429600	Weak transcription	Esophagus	oesophagus
4	chr12:4417400-4429600	Weak transcription	Pancreas	Pancrea
5	chr12:4417400-4429600	Weak transcription	HSMM	muscle
6	chr12:4417600-4429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:4417800-4429600	Weak transcription	Fetal Thymus	thymus
8	chr12:4417800-4429600	Weak transcription	Small Intestine	intestine
9	chr12:4418200-4429600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:4418600-4429600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:4418600-4429600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:4419000-4429600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:4419200-4429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:4421000-4429600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:4421200-4429600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:4422000-4429600	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:4422000-4429600	Weak transcription	Left Ventricle	heart
18	chr12:4423400-4429600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:4423600-4429600	Weak transcription	Fetal Stomach	stomach
20	chr12:4424000-4429600	Weak transcription	Brain Germinal Matrix	brain
21	chr12:4427800-4429600	Weak transcription	HSMMtube	muscle
22	chr12:4428800-4429600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:4429400-4429600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:4429400-4429600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:4429400-4429600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:4429400-4429600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:4429400-4429600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:4429400-4429600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:4429400-4429600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:4429400-4429600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:4429400-4429600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr12:4429400-4429600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:4429400-4429600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:4429400-4429600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:4429400-4429600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:4429400-4429600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:4429400-4429600	Enhancers	Liver	Liver
38	chr12:4429400-4429600	Enhancers	Colonic Mucosa	Colon
39	chr12:4429400-4429600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:4429400-4429600	Enhancers	Fetal Intestine Large	intestine
41	chr12:4429400-4429600	Enhancers	Fetal Kidney	kidney
42	chr12:4429400-4429600	Enhancers	Fetal Lung	lung
43	chr12:4429400-4429600	Active TSS	Placenta	Placenta
44	chr12:4429400-4429600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:4429400-4429600	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr12:4429400-4429600	Active TSS	HepG2	liver
47	chr12:4429400-4429600	Enhancers	NH-A	brain
48	chr12:4429400-4429800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:4429400-4429800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr12:4429400-4429800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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