Variant report

Variant	rs58556309
Chromosome Location	chr12:48534288-48534289
allele	G/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	POLR2A	chr12:48534221-48535215	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48530838..48533486-chr12:48533641..48536474,3	K562	blood:
2	chr12:48531947..48534928-chr12:48535593..48537352,2	MCF-7	breast:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10492082	0.86[EUR][1000 genomes]
rs1049392	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747529	0.81[ASN][1000 genomes]
rs10875733	0.92[EUR][1000 genomes]
rs10875739	0.81[ASN][1000 genomes]
rs10875741	0.87[ASN][1000 genomes]
rs10875744	0.90[ASN][1000 genomes]
rs10875752	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875754	0.81[ASN][1000 genomes]
rs10875759	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10875761	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11168373	0.92[EUR][1000 genomes]
rs11168378	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11168404	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168412	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168417	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168419	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168424	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168434	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168435	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168438	0.84[ASN][1000 genomes]
rs11168439	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11168442	0.88[AMR][1000 genomes]
rs11168443	0.86[AMR][1000 genomes]
rs11168444	0.88[AMR][1000 genomes]
rs11168445	0.88[AMR][1000 genomes]
rs11168446	0.88[AMR][1000 genomes]
rs11168447	0.88[AMR][1000 genomes]
rs11168448	0.86[AMR][1000 genomes]
rs11168453	0.88[AMR][1000 genomes]
rs11168454	0.86[AMR][1000 genomes]
rs11834818	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12228924	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12422355	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12425679	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426981	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2107640	0.80[ASN][1000 genomes]
rs2158515	0.90[ASN][1000 genomes]
rs2240306	0.91[EUR][1000 genomes]
rs2286020	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742075	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56097189	0.82[ASN][1000 genomes]
rs56129148	0.82[ASN][1000 genomes]
rs57430775	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58540891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59537300	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59667534	0.87[EUR][1000 genomes]
rs6580658	0.86[AMR][1000 genomes]
rs66507954	0.88[AMR][1000 genomes]
rs7132898	0.86[ASN][1000 genomes]
rs7133274	0.83[AMR][1000 genomes]
rs7136243	0.88[AMR][1000 genomes]
rs7136782	0.86[AMR][1000 genomes]
rs7136788	0.88[AMR][1000 genomes]
rs7302354	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303677	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304428	0.87[ASN][1000 genomes]
rs73104071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73304926	0.88[AMR][1000 genomes]
rs7484942	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7962390	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7962569	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8181670	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs886589	0.80[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	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	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv558790	chr12:48529168-48539888	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
12	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
17	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
19	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
26	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
27	chr12:48522400-48534400	Weak transcription	NHDF-Ad	bronchial
28	chr12:48523400-48546600	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:48523800-48540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:48524000-48536400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:48525000-48536400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:48525000-48539800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:48525400-48536600	Weak transcription	Right Atrium	heart
35	chr12:48525600-48546200	Strong transcription	A549	lung
36	chr12:48525800-48535600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:48526200-48547600	Strong transcription	Adipose Nuclei	Adipose
38	chr12:48526400-48540200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:48526400-48543600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:48527000-48536600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:48527200-48538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:48527600-48535000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:48528200-48535800	Weak transcription	Primary B cells from cord blood	blood
44	chr12:48529200-48535400	Weak transcription	Small Intestine	intestine
45	chr12:48529200-48536400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:48529200-48536600	Weak transcription	Pancreas	Pancrea
47	chr12:48529200-48542000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:48529400-48534400	Weak transcription	Dnd41	blood
49	chr12:48529400-48534600	Weak transcription	Esophagus	oesophagus
50	chr12:48529400-48535800	Weak transcription	Fetal Brain Male	brain

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