Variant report

Variant	rs12279202
Chromosome Location	chr11:9432090-9432091
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	chr11:9429811..9433973-chr11:9481355..9484368,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10082685	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10128708	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10840246	1.00[CEU][hapmap]
rs11042318	0.80[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11042323	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042324	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042325	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042346	1.00[AMR][1000 genomes];0.98[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]
rs11042379	0.81[EUR][1000 genomes]
rs11042401	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11601068	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11602025	1.00[CEU][hapmap]
rs11602056	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11607631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12272069	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12274646	0.81[EUR][1000 genomes]
rs12275828	0.83[AMR][1000 genomes]
rs12276413	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12282862	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12286949	0.92[GIH][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes]
rs12293264	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs12294461	0.92[AMR][1000 genomes]
rs1546	1.00[CEU][hapmap]
rs16906804	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]
rs28463550	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34485398	0.92[AMR][1000 genomes]
rs36048375	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4910052	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4910463	0.92[AMR][1000 genomes]
rs4910466	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4910467	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4910469	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs4910471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs55750964	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12279202	ZNF143	cis	multi-tissue	Pritchard
rs12279202	ZNF143	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9407600-9442000	Weak transcription	Fetal Brain Male	brain
2	chr11:9407600-9464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:9416000-9456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:9418200-9432200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:9419200-9446600	Weak transcription	Small Intestine	intestine
6	chr11:9419600-9432400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr11:9419600-9471000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:9419800-9444200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:9420000-9440200	Weak transcription	Fetal Kidney	kidney
10	chr11:9420200-9432200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:9420400-9432200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:9420600-9442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:9420600-9450400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:9421000-9471200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:9421600-9436400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:9423000-9470400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:9424200-9470400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:9424800-9437800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:9424800-9438200	Strong transcription	Fetal Thymus	thymus
20	chr11:9424800-9438200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:9424800-9468600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:9424800-9469000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:9424800-9470600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:9425000-9434000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:9425000-9468200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:9425000-9468400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr11:9425200-9467200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:9425400-9438800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:9425600-9446800	Weak transcription	Colonic Mucosa	Colon
30	chr11:9425800-9468000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:9426200-9471600	Strong transcription	Dnd41	blood
32	chr11:9426400-9443000	Strong transcription	Hela-S3	cervix
33	chr11:9426800-9437800	Strong transcription	HepG2	liver
34	chr11:9426800-9468400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr11:9426800-9470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:9427000-9433200	Strong transcription	HSMM	muscle
37	chr11:9427000-9433400	Strong transcription	Osteobl	bone
38	chr11:9427200-9466800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:9427600-9471000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:9427800-9432200	Weak transcription	Psoas Muscle	Psoas
41	chr11:9428200-9433400	Strong transcription	HMEC	breast
42	chr11:9428800-9435800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr11:9429400-9433800	Strong transcription	K562	blood
44	chr11:9429600-9433400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:9429800-9433200	Strong transcription	GM12878-XiMat	blood
46	chr11:9429800-9433600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr11:9429800-9434200	Strong transcription	Liver	Liver
48	chr11:9429800-9437600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr11:9429800-9443000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:9429800-9469000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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