Variant report

Variant	rs10875908
Chromosome Location	chr12:49400505-49400506
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49379485..49382055-chr12:49399964..49402109,2	MCF-7	breast:
2	chr12:49390603..49394865-chr12:49395546..49401151,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181418	Chromatin interaction
ENSG00000257913	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10459221	0.81[ASN][1000 genomes]
rs10459232	0.81[ASN][1000 genomes]
rs1054442	0.96[ASN][1000 genomes]
rs10747559	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10783299	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783300	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783301	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875906	0.94[ASN][1000 genomes]
rs10875910	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875911	1.00[ASN][1000 genomes]
rs10875912	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10875913	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875914	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875915	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875917	0.81[ASN][1000 genomes]
rs10875918	0.80[ASN][1000 genomes]
rs11168822	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168827	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168838	0.83[ASN][1000 genomes]
rs11168839	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168850	0.80[ASN][1000 genomes]
rs1138908	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614738	0.96[ASN][1000 genomes]
rs12580349	0.86[ASN][1000 genomes]
rs12821008	0.80[ASN][1000 genomes]
rs2117029	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241726	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293445	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293446	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304275	0.87[ASN][1000 genomes]
rs34436857	0.90[ASN][1000 genomes]
rs3741619	0.95[ASN][1000 genomes]
rs3741622	0.88[ASN][1000 genomes]
rs3782357	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300136	0.80[ASN][1000 genomes]
rs7969091	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
rs10875908	DDN	cis	Muscle Skeletal	GTEx
rs10875908	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs10875908	RP11-386G11.5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49394600-49401400	Strong transcription	Osteobl	bone
2	chr12:49394800-49403200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:49394800-49405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:49395000-49401400	Strong transcription	GM12878-XiMat	blood
5	chr12:49395000-49402200	Weak transcription	Stomach Mucosa	stomach
6	chr12:49395000-49403000	Strong transcription	NHDF-Ad	bronchial
7	chr12:49395400-49407000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:49395400-49407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:49395400-49411600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:49395600-49402600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:49395600-49407600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:49396000-49411600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:49396600-49407600	Weak transcription	Fetal Heart	heart
14	chr12:49396800-49402600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:49396800-49411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:49397000-49411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:49397000-49411400	Weak transcription	Fetal Brain Male	brain
18	chr12:49397200-49411600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:49397600-49400600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:49397600-49402200	Weak transcription	HUVEC	blood vessel
21	chr12:49397600-49411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:49399000-49402200	Weak transcription	HepG2	liver
23	chr12:49399200-49404000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:49399200-49411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:49399400-49402200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:49399400-49402200	Weak transcription	A549	lung
27	chr12:49399400-49404000	Weak transcription	NHEK	skin
28	chr12:49399400-49405000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:49399400-49405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:49399400-49405200	Weak transcription	Right Ventricle	heart
31	chr12:49399400-49405600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:49399600-49401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:49399600-49402000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:49399600-49402000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:49399600-49402200	Weak transcription	Primary B cells from cord blood	blood
36	chr12:49399600-49402200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:49399600-49402200	Weak transcription	Aorta	Aorta
38	chr12:49399600-49402200	Weak transcription	Psoas Muscle	Psoas
39	chr12:49399600-49402200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:49399600-49402400	Weak transcription	Adipose Nuclei	Adipose
41	chr12:49399600-49402600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:49399600-49403000	Weak transcription	Fetal Lung	lung
43	chr12:49399600-49403800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:49399600-49403800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:49399600-49404000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:49399600-49404000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:49399600-49404000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:49399600-49404000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:49399600-49404000	Weak transcription	Fetal Brain Female	brain
50	chr12:49399600-49404000	Weak transcription	Fetal Intestine Small	intestine

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