Variant report

Variant	rs73304926
Chromosome Location	chr12:48578442-48578443
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	SIN3A	chr12:48576618-48579251	H1-hESC	embryonic stem cell:	n/a	chr12:48577451-48577460
2	ELF1	chr12:48577870-48578524	GM12878	blood:	n/a	n/a
3	MAX	chr12:48577897-48578780	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr12:48576436-48579525	SK-N-SH	brain:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
5	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
6	MAX	chr12:48577849-48578831	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr12:48577847-48578788	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr12:48578404-48579318	H1-neurons	neurons:	n/a	n/a
9	CTBP2	chr12:48576803-48578719	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:48576694-48580496	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr12:48578332-48580491	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48578276..48580987-chr12:48583534..48585807,2	K562	blood:
2	chr12:48548408..48551386-chr12:48576630..48579457,3	K562	blood:
3	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:
4	chr12:48549998..48552316-chr12:48577251..48580205,2	MCF-7	breast:
5	chr12:48577879..48579746-chr12:48586715..48588244,2	K562	blood:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000269514	Chromatin interaction

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];0.88[ASN][1000 genomes]
rs10875754	0.85[ASN][1000 genomes]
rs10875759	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875761	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875765	0.99[ASN][1000 genomes]
rs10875766	0.91[ASN][1000 genomes]
rs11168424	0.85[AMR][1000 genomes]
rs11168434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168438	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11168439	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168443	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168444	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168446	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168447	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168448	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168453	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168454	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425679	0.88[AMR][1000 genomes]
rs2171643	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2286020	0.88[AMR][1000 genomes]
rs56097189	0.95[ASN][1000 genomes]
rs57430775	0.86[AMR][1000 genomes]
rs58540891	0.88[AMR][1000 genomes]
rs58556309	0.88[AMR][1000 genomes]
rs59537300	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580658	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66507954	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132898	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7133274	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136243	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136782	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73104071	0.88[AMR][1000 genomes]
rs73105950	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484942	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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
rs73304926	C12orf68	cis	Esophagus Mucosa	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:48576200-48579000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:48576200-48579000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:48576400-48578800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:48576400-48578800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr12:48576600-48578600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:48576600-48578600	Bivalent/Poised TSS	HSMM	muscle
9	chr12:48576600-48578800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
10	chr12:48576600-48579000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
13	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr12:48576800-48578600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr12:48576800-48578600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr12:48576800-48578800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:48576800-48580000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:48577200-48578600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:48577200-48578600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
20	chr12:48577200-48578600	Bivalent/Poised TSS	Psoas Muscle	Psoas
21	chr12:48577200-48578800	Active TSS	Ovary	ovary
22	chr12:48577200-48579000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:48577400-48578600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:48577400-48578600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:48577400-48578600	Bivalent/Poised TSS	Left Ventricle	heart
26	chr12:48577400-48578800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
30	chr12:48577400-48579000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:48577600-48578600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
32	chr12:48577600-48578600	Bivalent/Poised TSS	NHDF-Ad	bronchial
33	chr12:48577600-48578800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:48577600-48578800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr12:48577800-48578600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr12:48577800-48578600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr12:48577800-48578800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
38	chr12:48577800-48578800	Bivalent/Poised TSS	NH-A	brain
39	chr12:48577800-48579000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:48577800-48579000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:48577800-48579000	Bivalent Enhancer	Fetal Thymus	thymus
42	chr12:48577800-48579200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr12:48578000-48578600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:48578000-48578600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:48578000-48578600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr12:48578000-48578600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
47	chr12:48578000-48578600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:48578000-48578600	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr12:48578000-48578600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr12:48578000-48578600	Flanking Active TSS	Brain Substantia Nigra	brain

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