Variant report

Variant	rs11602056
Chromosome Location	chr11:9541423-9541424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9537904..9540865-chr11:9540885..9544510,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082685	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10840246	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11042318	0.80[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs11042365	0.84[EUR][1000 genomes]
rs11042367	0.84[EUR][1000 genomes]
rs11042379	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042401	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042402	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11600094	0.86[AMR][1000 genomes]
rs11600357	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11602025	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11607631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274646	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12274655	0.86[AMR][1000 genomes]
rs12279202	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12280032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280819	0.92[AMR][1000 genomes]
rs12284187	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12284407	0.86[AMR][1000 genomes]
rs12285570	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12286949	0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12292907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12293264	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12293634	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12293911	0.87[EUR][1000 genomes]
rs12419780	0.86[AMR][1000 genomes]
rs1546	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16906804	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs36048375	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4910052	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4910054	0.81[AMR][1000 genomes]
rs4910466	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910467	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4910469	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs4910471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910475	0.86[AMR][1000 genomes]
rs56116319	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56320702	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9988896	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs11602056	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	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:9530200-9544600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:9531000-9550800	Weak transcription	Pancreas	Pancrea
11	chr11:9532600-9546400	Weak transcription	Stomach Mucosa	stomach
12	chr11:9533400-9541600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:9533400-9550600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr11:9534000-9541600	Strong transcription	Liver	Liver
15	chr11:9534000-9543800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:9534000-9544600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:9534600-9545800	Weak transcription	Fetal Heart	heart
18	chr11:9534600-9546800	Weak transcription	Gastric	stomach
19	chr11:9534600-9556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:9535000-9548400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:9535000-9548800	Weak transcription	NHEK	skin
22	chr11:9535200-9548800	Weak transcription	Fetal Brain Male	brain
23	chr11:9535200-9551200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:9535400-9550800	Weak transcription	Brain Anterior Caudate	brain
25	chr11:9535800-9548600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:9535800-9549000	Weak transcription	Aorta	Aorta
27	chr11:9535800-9550800	Weak transcription	Esophagus	oesophagus
28	chr11:9535800-9554800	Weak transcription	Ovary	ovary
29	chr11:9536000-9543400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:9536200-9550600	Weak transcription	HSMMtube	muscle
31	chr11:9536200-9552400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:9536400-9554800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:9537400-9551200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:9538000-9543400	Weak transcription	Thymus	Thymus
35	chr11:9538000-9546800	Weak transcription	Lung	lung
36	chr11:9538000-9550800	Weak transcription	Right Ventricle	heart
37	chr11:9538200-9545600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr11:9538200-9545800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:9538200-9546800	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:9538200-9547400	Weak transcription	Spleen	Spleen
41	chr11:9538200-9548600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr11:9538200-9548600	Weak transcription	Hela-S3	cervix
43	chr11:9538200-9549000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr11:9538200-9550400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:9538200-9550800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:9538400-9545800	Weak transcription	NH-A	brain
47	chr11:9538400-9548600	Weak transcription	A549	lung
48	chr11:9538400-9548800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:9538600-9545000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:9538600-9545600	Weak transcription	NHDF-Ad	bronchial

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