Variant report

Variant	rs12274646
Chromosome Location	chr11:9496857-9496858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9479692..9486524-chr11:9491765..9498081,14	K562	blood:
2	chr11:9496196..9499185-chr11:9501862..9504317,2	K562	blood:
3	chr11:9480422..9483658-chr11:9496171..9498289,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10082685	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10128708	0.83[EUR][1000 genomes]
rs1048487	0.86[AFR][1000 genomes]
rs10840246	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042346	0.83[EUR][1000 genomes]
rs11042361	0.81[EUR][1000 genomes]
rs11042363	0.81[EUR][1000 genomes]
rs11042365	0.94[EUR][1000 genomes]
rs11042367	0.94[EUR][1000 genomes]
rs11042379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042401	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042402	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11600357	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11602025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11602056	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11607631	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12279202	0.81[EUR][1000 genomes]
rs12280032	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12280301	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12284187	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12285570	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12292907	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12293264	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12293634	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1546	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34972213	0.83[AFR][1000 genomes]
rs36048375	0.83[EUR][1000 genomes]
rs4910052	0.83[EUR][1000 genomes]
rs4910466	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4910467	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4910469	0.86[EUR][1000 genomes]
rs4910471	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55750964	0.83[EUR][1000 genomes]
rs56067293	0.81[AFR][1000 genomes]
rs56080598	1.00[AFR][1000 genomes]
rs56116319	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56320702	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57050521	0.83[AFR][1000 genomes]
rs57731483	0.81[AFR][1000 genomes]
rs58580896	0.81[AFR][1000 genomes]
rs58602953	1.00[AFR][1000 genomes]
rs58904027	0.86[AFR][1000 genomes]
rs59113683	1.00[AFR][1000 genomes]
rs59158354	0.83[AFR][1000 genomes]
rs59571955	1.00[AFR][1000 genomes]
rs60482254	0.80[AFR][1000 genomes]
rs73404370	0.81[AFR][1000 genomes]
rs73404376	0.81[AFR][1000 genomes]
rs73404388	0.81[AFR][1000 genomes]
rs73404392	0.91[AFR][1000 genomes]
rs73404395	0.81[AFR][1000 genomes]
rs73406215	0.81[AFR][1000 genomes]
rs73406223	0.81[AFR][1000 genomes]
rs73406243	0.86[AFR][1000 genomes]
rs73406255	0.86[AFR][1000 genomes]
rs73406259	0.86[AFR][1000 genomes]
rs73406261	1.00[AFR][1000 genomes]
rs73406268	1.00[AFR][1000 genomes]
rs73406269	1.00[AFR][1000 genomes]
rs73406286	0.83[AFR][1000 genomes]
rs73406291	0.83[AFR][1000 genomes]
rs9988896	0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12274646	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	chr11:9483400-9499800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:9483600-9499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:9483600-9499400	Weak transcription	Pancreas	Pancrea
4	chr11:9483600-9518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:9484000-9499600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:9484200-9499800	Weak transcription	Brain Angular Gyrus	brain
7	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:9485200-9520000	Weak transcription	Stomach Mucosa	stomach
9	chr11:9485400-9499600	Weak transcription	A549	lung
10	chr11:9485600-9499800	Weak transcription	Hela-S3	cervix
11	chr11:9489600-9524000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:9489800-9523400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:9490800-9497800	Strong transcription	Primary T cells from cord blood	blood
14	chr11:9491200-9497800	Strong transcription	Primary B cells from cord blood	blood
15	chr11:9491200-9497800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:9491400-9498200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr11:9491400-9506200	Strong transcription	Liver	Liver
18	chr11:9491400-9525400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:9491600-9497400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:9491600-9497800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:9491600-9497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:9491600-9497800	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:9491600-9497800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:9491600-9498200	Strong transcription	Fetal Lung	lung
26	chr11:9491600-9502600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:9492000-9498200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:9492000-9498200	Strong transcription	Left Ventricle	heart
29	chr11:9492000-9506000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:9492000-9527200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:9492200-9497000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:9492200-9497800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:9492200-9497800	Strong transcription	Adipose Nuclei	Adipose
34	chr11:9492200-9503000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:9492200-9525400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:9492400-9497200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:9492600-9498800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:9492600-9502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:9492600-9505800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:9492800-9497600	Strong transcription	Fetal Intestine Large	intestine
41	chr11:9492800-9497800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:9492800-9498400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:9492800-9498400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:9492800-9499600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr11:9492800-9507800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:9492800-9527800	Strong transcription	Fetal Stomach	stomach
47	chr11:9493000-9498000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:9493000-9498000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:9493000-9498400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr11:9493200-9497400	Strong transcription	Small Intestine	intestine

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