Variant report

Variant	rs59537300
Chromosome Location	chr12:48576606-48576607
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	NRF1	chr12:48576340-48577481	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr12:48576436-48579525	SK-N-SH	brain:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
3	RFX5	chr12:48575846-48577828	SK-N-SH	brain:	n/a	chr12:48577379-48577396 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577343-48577360 chr12:48577344-48577359 chr12:48577341-48577356 chr12:48577380-48577395 chr12:48577344-48577359 chr12:48577380-48577395
4	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
5	IRF1	chr12:48576378-48576707	K562	blood:	n/a	n/a
6	CTCF	chr12:48576460-48576610	AG09319	gingival:	n/a	n/a
7	IRF1	chr12:48576486-48576934	K562	blood:	n/a	n/a
8	REST	chr12:48576590-48577683	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
9	CTCF	chr12:48576485-48578340	SK-N-SH	brain:	n/a	n/a
10	RUNX3	chr12:48576396-48576822	GM12878	blood:	n/a	n/a
11	CTCF	chr12:48576593-48577606	HCT-116	colon:	n/a	n/a
12	CTCF	chr12:48576494-48578211	A549	lung:	n/a	n/a
13	TCF12	chr12:48576583-48577782	A549	lung:	n/a	n/a

Variant related genes	Relation type
C12orf68	TF binding region
ASB8	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1049392	0.85[AMR][1000 genomes]
rs10875752	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875754	0.86[ASN][1000 genomes]
rs10875759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875761	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875765	0.98[ASN][1000 genomes]
rs10875766	0.90[ASN][1000 genomes]
rs11168424	0.85[AMR][1000 genomes]
rs11168434	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168438	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11168439	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168442	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168443	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168444	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168445	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168446	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168448	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168453	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168454	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425679	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2171643	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2286020	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56097189	0.96[ASN][1000 genomes]
rs57430775	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58540891	0.88[AMR][1000 genomes]
rs58556309	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6580658	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66507954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132898	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7133274	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136243	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136782	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73104071	0.88[AMR][1000 genomes]
rs73105950	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73304926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484942	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962390	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962569	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59537300	C12orf68	cis	Esophagus Mucosa	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576000-48576800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:48576200-48576800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
3	chr12:48576200-48576800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr12:48576200-48576800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
5	chr12:48576200-48576800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr12:48576200-48576800	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr12:48576200-48576800	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr12:48576200-48576800	Flanking Active TSS	NHDF-Ad	bronchial
9	chr12:48576200-48577000	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr12:48576200-48577000	Bivalent Enhancer	Fetal Lung	lung
11	chr12:48576200-48577200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:48576200-48577200	Flanking Active TSS	HMEC	breast
13	chr12:48576200-48577200	Flanking Bivalent TSS/Enh	NHEK	skin
14	chr12:48576200-48577400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:48576200-48578000	Active TSS	Brain Anterior Caudate	brain
16	chr12:48576200-48578000	Active TSS	Right Atrium	heart
17	chr12:48576200-48578200	Active TSS	Aorta	Aorta
18	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:48576200-48579000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:48576200-48579000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:48576400-48576800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr12:48576400-48576800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr12:48576400-48576800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
25	chr12:48576400-48576800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:48576400-48576800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:48576400-48576800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr12:48576400-48576800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:48576400-48576800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48576400-48576800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:48576400-48576800	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr12:48576400-48576800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:48576400-48576800	Flanking Active TSS	Fetal Brain Female	brain
34	chr12:48576400-48576800	Flanking Active TSS	NH-A	brain
35	chr12:48576400-48577000	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr12:48576400-48577000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:48576400-48577000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr12:48576400-48577000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr12:48576400-48577000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:48576400-48577000	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
41	chr12:48576400-48577000	Flanking Active TSS	Fetal Brain Male	brain
42	chr12:48576400-48577000	Enhancers	Small Intestine	intestine
43	chr12:48576400-48577000	Flanking Active TSS	GM12878-XiMat	blood
44	chr12:48576400-48577000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr12:48576400-48577200	Flanking Active TSS	Ovary	ovary
47	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
48	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
49	chr12:48576400-48577400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:48576400-48577400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links