Variant report

Variant	rs10875880
Chromosome Location	chr12:49244263-49244264
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49244149..49247655-chr12:49370994..49373492,3	K562	blood:
2	chr12:49243168..49245554-chr12:49387627..49389911,2	MCF-7	breast:
3	chr12:49243837..49250262-chr12:49279824..49286856,16	MCF-7	breast:
4	chr12:49226521..49228044-chr12:49243718..49245705,2	MCF-7	breast:
5	chr12:49207378..49214966-chr12:49243991..49247655,21	MCF-7	breast:
6	chr12:49243936..49245890-chr12:49261008..49263611,2	K562	blood:
7	chr12:49203980..49213270-chr12:49239370..49250118,15	MCF-7	breast:
8	chr12:49244090..49248564-chr12:49349147..49352476,5	MCF-7	breast:
9	chr12:49243113..49245628-chr12:49452300..49454893,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199394	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000134287	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1045340	0.92[ASN][1000 genomes]
rs1057908	0.96[ASN][1000 genomes]
rs10875879	1.00[ASN][1000 genomes]
rs11168753	0.80[ASN][1000 genomes]
rs11168758	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2453471	0.93[ASN][1000 genomes]
rs2453472	0.93[ASN][1000 genomes]
rs2453482	1.00[ASN][1000 genomes]
rs59128273	0.96[ASN][1000 genomes]
rs61941108	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61941109	0.81[EUR][1000 genomes]
rs7164	0.91[ASN][1000 genomes]
rs954	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875880	DDX23	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49216800-49244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:49227000-49244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:49234000-49244400	Weak transcription	Psoas Muscle	Psoas
4	chr12:49234200-49244400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:49237000-49244400	Strong transcription	Fetal Intestine Large	intestine
6	chr12:49237000-49244600	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:49238200-49244600	Weak transcription	HSMMtube	muscle
8	chr12:49238400-49244400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:49238400-49244800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:49239600-49244400	Weak transcription	Pancreas	Pancrea
11	chr12:49239600-49244400	Weak transcription	Right Ventricle	heart
12	chr12:49239600-49245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:49239800-49244400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:49239800-49244400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:49239800-49244400	Weak transcription	Fetal Brain Female	brain
16	chr12:49239800-49244400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:49239800-49244400	Weak transcription	HSMM	muscle
18	chr12:49239800-49244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:49239800-49244600	Weak transcription	Esophagus	oesophagus
20	chr12:49239800-49244600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:49239800-49244800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:49239800-49244800	Weak transcription	Left Ventricle	heart
23	chr12:49239800-49245200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:49239800-49245400	Weak transcription	Aorta	Aorta
25	chr12:49240000-49244400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:49240000-49244400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:49240000-49244400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:49240000-49244400	Weak transcription	Gastric	stomach
29	chr12:49240000-49244400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:49240000-49244600	Weak transcription	Fetal Brain Male	brain
31	chr12:49240200-49244400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:49240200-49244400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:49240400-49244400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:49240400-49244400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:49240400-49244400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:49240400-49244800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:49240800-49244400	Weak transcription	NH-A	brain
38	chr12:49240800-49244600	Weak transcription	Placenta	Placenta
39	chr12:49241000-49244400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:49241000-49244400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:49241000-49244400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:49241200-49244400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:49241200-49244400	Weak transcription	Lung	lung
44	chr12:49241200-49244600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:49241600-49244400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:49242800-49244400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:49242800-49244600	Genic enhancers	Spleen	Spleen
48	chr12:49242800-49244800	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr12:49243200-49244400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr12:49243200-49244400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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