Variant report

Variant	rs12282862
Chromosome Location	chr11:9474786-9474787
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	chr11:9474328..9476179-chr11:9477857..9479855,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10128708	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042323	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042324	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042325	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042346	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042361	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042363	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042365	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042367	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11601068	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12272069	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12275828	0.83[AMR][1000 genomes]
rs12276413	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12279202	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12286949	0.92[AMR][1000 genomes]
rs12294461	0.92[AMR][1000 genomes]
rs16906804	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28463550	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34485398	0.92[AMR][1000 genomes]
rs36048375	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4910052	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4910463	0.92[AMR][1000 genomes]
rs55750964	1.00[AMR][1000 genomes];0.94[EUR][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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv825762	chr11:9470175-9479714	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12282862	ZNF143	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9452800-9480000	Weak transcription	Fetal Brain Male	brain
2	chr11:9457800-9480600	Weak transcription	Psoas Muscle	Psoas
3	chr11:9461800-9474800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:9462200-9481000	Weak transcription	NHLF	lung
5	chr11:9463400-9481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:9463800-9481000	Weak transcription	NHDF-Ad	bronchial
7	chr11:9464800-9480800	Weak transcription	HSMMtube	muscle
8	chr11:9465000-9480800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:9465000-9480800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:9465000-9481000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr11:9465200-9476000	Weak transcription	Aorta	Aorta
12	chr11:9465200-9481000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:9465200-9481200	Weak transcription	Ovary	ovary
14	chr11:9465400-9481000	Weak transcription	Brain Substantia Nigra	brain
15	chr11:9465400-9481000	Weak transcription	K562	blood
16	chr11:9465800-9480600	Weak transcription	Esophagus	oesophagus
17	chr11:9465800-9481000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:9466400-9480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:9466600-9475200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:9466600-9480800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr11:9466800-9480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:9466800-9481000	Weak transcription	Fetal Lung	lung
23	chr11:9467000-9480800	Weak transcription	Lung	lung
24	chr11:9467400-9480800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:9468000-9481000	Weak transcription	Fetal Heart	heart
26	chr11:9468000-9481000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:9468000-9481000	Weak transcription	NH-A	brain
28	chr11:9468200-9481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:9470200-9475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:9470200-9476000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:9470200-9480800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:9470200-9480800	Weak transcription	Left Ventricle	heart
33	chr11:9470200-9480800	Weak transcription	HSMM	muscle
34	chr11:9470200-9480800	Weak transcription	NHEK	skin
35	chr11:9470200-9481000	Weak transcription	A549	lung
36	chr11:9470200-9481000	Weak transcription	HUVEC	blood vessel
37	chr11:9470200-9481200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:9470400-9480800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:9470400-9480800	Weak transcription	HMEC	breast
40	chr11:9470400-9481000	Weak transcription	Osteobl	bone
41	chr11:9470600-9480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:9470800-9480800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:9471000-9480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:9471000-9480800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:9471600-9480200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:9472000-9480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:9472600-9475200	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr11:9473200-9480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:9473400-9474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:9473600-9480800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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