Variant report

Variant	rs12316559
Chromosome Location	chr12:9219729-9219730
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	CEBPB	chr12:9219366-9219864	A549	lung:	n/a	chr12:9219564-9219575
2	FOS	chr12:9219622-9219913	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
4	MBD4	chr12:9218319-9219866	HepG2	liver:	n/a	n/a
5	STAT3	chr12:9219617-9219837	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:9216806-9219983	HepG2	liver:	n/a	n/a
7	CHD2	chr12:9217996-9219810	HepG2	liver:	n/a	n/a
8	FOS	chr12:9219688-9219854	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:9216389-9221070	HepG2	liver:	n/a	n/a
10	MYBL2	chr12:9218472-9220191	HepG2	liver:	n/a	n/a
11	CEBPB	chr12:9219389-9219756	IMR90	lung:	n/a	chr12:9219564-9219575
12	BRCA1	chr12:9219679-9219945	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:9217415-9220251	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:9216589-9220417	HepG2	liver:	n/a	n/a
15	MBD4	chr12:9218464-9220244	HepG2	liver:	n/a	n/a
16	FOS	chr12:9219619-9219947	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr12:9218989-9219886	HepG2	liver:	n/a	n/a
18	NFIC	chr12:9218583-9220189	HepG2	liver:	n/a	n/a
19	CEBPB	chr12:9219388-9219817	Hela-S3	cervix:	n/a	chr12:9219564-9219575
20	STAT3	chr12:9219656-9220014	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr12:9219619-9219948	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:9216161-9220988	HepG2	liver:	n/a	n/a
23	CEBPB	chr12:9219386-9219734	H1-hESC	embryonic stem cell:	n/a	chr12:9219564-9219575
24	RFX5	chr12:9219647-9219885	HepG2	liver:	n/a	n/a
25	CEBPB	chr12:9219357-9219757	HepG2	liver:	n/a	chr12:9219564-9219575
26	MYC	chr12:9219619-9219848	MCF10A-Er-Src	breast:	n/a	n/a
27	MYC	chr12:9219622-9219946	MCF10A-Er-Src	breast:	n/a	n/a
28	CEBPB	chr12:9219320-9219803	A549	lung:	n/a	chr12:9219564-9219575

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9218102..9220634-chr12:9230847..9232385,2	MCF-7	breast:
2	chr12:9218454..9221005-chr12:9232709..9234704,2	K562	blood:

Variant related genes	Relation type
LINC00612	TF binding region
ENSG00000175899	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12300614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12303841	0.83[AFR][1000 genomes]
rs12305636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314690	1.00[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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:9217600-9223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:9217800-9220400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
5	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:9218000-9220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:9218200-9220000	Enhancers	Hela-S3	cervix
10	chr12:9218200-9220000	Enhancers	HMEC	breast
11	chr12:9218200-9223000	Weak transcription	Aorta	Aorta
12	chr12:9218200-9223200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:9218200-9224200	Weak transcription	Ovary	ovary
14	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
16	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
17	chr12:9218400-9219800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:9218400-9220000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:9218400-9220200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:9218400-9220200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:9218400-9220400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:9218400-9223800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:9218400-9224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:9218400-9224200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:9218400-9224600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:9218400-9228600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:9218400-9230800	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:9218400-9231000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
30	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:9218600-9219800	Weak transcription	Adipose Nuclei	Adipose
34	chr12:9218600-9220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:9218600-9220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:9218600-9225000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:9218600-9229400	Weak transcription	Colonic Mucosa	Colon
38	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:9218800-9219800	Weak transcription	Fetal Lung	lung
42	chr12:9218800-9219800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:9218800-9220800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:9218800-9225000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:9218800-9230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
48	chr12:9219000-9220000	Enhancers	Fetal Intestine Small	intestine
49	chr12:9219000-9220000	Enhancers	HepG2	liver
50	chr12:9219000-9220200	Weak transcription	Left Ventricle	heart

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