Variant report

Variant	rs11042402
Chromosome Location	chr11:9535250-9535251
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9534694..9537562-chr11:9542413..9544187,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10082685	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840246	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042365	0.81[EUR][1000 genomes]
rs11042367	0.81[EUR][1000 genomes]
rs11042379	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042401	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11600094	0.86[AMR][1000 genomes]
rs11600357	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11602025	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11602056	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11607631	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12274646	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12274655	0.86[AMR][1000 genomes]
rs12280032	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12280301	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12280819	0.92[AMR][1000 genomes]
rs12284187	1.00[AMR][1000 genomes]
rs12284407	0.86[AMR][1000 genomes]
rs12285570	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12292907	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12293264	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12293634	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12293911	0.83[EUR][1000 genomes]
rs12419780	0.86[AMR][1000 genomes]
rs1546	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910054	0.81[AMR][1000 genomes]
rs4910466	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910467	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910469	0.93[EUR][1000 genomes]
rs4910471	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4910475	0.86[AMR][1000 genomes]
rs56116319	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56320702	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9988896	0.93[AMR][1000 genomes];0.96[EUR][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	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042402	ZNF143	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:9521000-9545200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:9523400-9550800	Weak transcription	Colonic Mucosa	Colon
5	chr11:9523400-9551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:9528000-9540000	Strong transcription	Fetal Thymus	thymus
7	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:9530000-9541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:9530200-9538400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:9530200-9538800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:9530200-9539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:9530200-9540000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:9530200-9540200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:9530200-9541400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:9530200-9541400	Strong transcription	Adipose Nuclei	Adipose
17	chr11:9530200-9544600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:9530400-9539400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:9531000-9535800	Weak transcription	NHLF	lung
21	chr11:9531000-9550800	Weak transcription	Pancreas	Pancrea
22	chr11:9531600-9539600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:9532600-9546400	Weak transcription	Stomach Mucosa	stomach
24	chr11:9533400-9541600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr11:9533400-9550600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr11:9533600-9535600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:9533600-9536000	Strong transcription	HSMM	muscle
28	chr11:9533600-9536400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:9533600-9536600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:9533600-9536600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:9533600-9537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:9533600-9538400	Strong transcription	Colon Smooth Muscle	Colon
33	chr11:9533600-9538400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:9533600-9539200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:9533600-9539200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:9533600-9539800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:9533600-9539800	Strong transcription	Fetal Lung	lung
38	chr11:9533600-9540000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:9533600-9540000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:9533600-9540000	Strong transcription	K562	blood
41	chr11:9533600-9541200	Strong transcription	Primary B cells from cord blood	blood
42	chr11:9533600-9541400	Strong transcription	Primary T cells from cord blood	blood
43	chr11:9533800-9536000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:9533800-9539000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:9533800-9540200	Strong transcription	GM12878-XiMat	blood
46	chr11:9534000-9535400	Strong transcription	Brain Anterior Caudate	brain
47	chr11:9534000-9535600	Genic enhancers	Fetal Intestine Large	intestine
48	chr11:9534000-9535800	Strong transcription	Aorta	Aorta
49	chr11:9534000-9535800	Strong transcription	Esophagus	oesophagus
50	chr11:9534000-9535800	Strong transcription	Ovary	ovary

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