Variant report

Variant	rs10875910
Chromosome Location	chr12:49402393-49402394
allele	C/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	POLR2A	chr12:49402237-49402559	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49401638..49404113-chr12:49657621..49659917,2	K562	blood:
2	chr12:49396774..49398667-chr12:49400823..49402864,2	MCF-7	breast:
3	chr12:49401314..49403138-chr12:49656982..49659121,2	K562	blood:
4	chr12:49349394..49351523-chr12:49401057..49403501,2	K562	blood:

Variant related genes	Relation type
PRKAG1	TF binding region
ENSG00000272822	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000181929	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10459221	0.81[ASN][1000 genomes]
rs10459232	0.81[ASN][1000 genomes]
rs1054442	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10747559	0.86[ASN][1000 genomes]
rs10783299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10783300	1.00[ASN][1000 genomes]
rs10783301	0.89[ASN][1000 genomes]
rs10875906	0.94[ASN][1000 genomes]
rs10875908	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875911	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10875915	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875917	0.81[ASN][1000 genomes]
rs10875918	0.80[ASN][1000 genomes]
rs11168822	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168827	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11168838	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168839	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168850	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1138908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11614738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12580349	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12821008	0.80[ASN][1000 genomes]
rs2117029	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2241726	0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293445	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2293446	0.99[ASN][1000 genomes]
rs2304275	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34436857	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3741619	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3741622	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6580698	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6580699	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7296288	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7300136	0.80[ASN][1000 genomes]
rs7969091	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs876333	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10875910	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs10875910	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs10875910	DDN	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49394800-49403200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:49394800-49405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:49395000-49403000	Strong transcription	NHDF-Ad	bronchial
4	chr12:49395400-49407000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr12:49395400-49407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:49395400-49411600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:49395600-49402600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:49395600-49407600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:49396000-49411600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:49396600-49407600	Weak transcription	Fetal Heart	heart
11	chr12:49396800-49402600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:49396800-49411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:49397000-49411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:49397000-49411400	Weak transcription	Fetal Brain Male	brain
15	chr12:49397200-49411600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:49397600-49411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:49399200-49404000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:49399200-49411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:49399400-49404000	Weak transcription	NHEK	skin
20	chr12:49399400-49405000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:49399400-49405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:49399400-49405200	Weak transcription	Right Ventricle	heart
23	chr12:49399400-49405600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:49399600-49402400	Weak transcription	Adipose Nuclei	Adipose
25	chr12:49399600-49402600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:49399600-49403000	Weak transcription	Fetal Lung	lung
27	chr12:49399600-49403800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:49399600-49403800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:49399600-49404000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49399600-49404000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:49399600-49404000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:49399600-49404000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:49399600-49404000	Weak transcription	Fetal Brain Female	brain
34	chr12:49399600-49404000	Weak transcription	Fetal Intestine Small	intestine
35	chr12:49399600-49404000	Weak transcription	Lung	lung
36	chr12:49399600-49404000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:49399600-49404000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:49399600-49404000	Weak transcription	Thymus	Thymus
39	chr12:49399600-49404000	Weak transcription	HMEC	breast
40	chr12:49399600-49404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:49399600-49404200	Weak transcription	Colonic Mucosa	Colon
42	chr12:49399600-49404200	Weak transcription	Gastric	stomach
43	chr12:49399600-49404200	Weak transcription	Spleen	Spleen
44	chr12:49399600-49405400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:49399600-49405400	Weak transcription	NHLF	lung
46	chr12:49399600-49405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:49399600-49405800	Weak transcription	Esophagus	oesophagus
48	chr12:49399600-49406000	Weak transcription	Small Intestine	intestine
49	chr12:49399600-49407200	Weak transcription	K562	blood
50	chr12:49399600-49411000	Weak transcription	Pancreas	Pancrea

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