Variant report

Variant	rs12190280
Chromosome Location	chr6:88038008-88038009
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	chr6:88031398..88035229-chr6:88037396..88042297,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164411	Chromatin interaction
ENSG00000226524	Chromatin interaction
ENSG00000111850	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs107689	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs107690	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1080596	0.80[EUR][1000 genomes]
rs1201409	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12176253	0.84[ASN][1000 genomes]
rs12207825	0.80[EUR][1000 genomes]
rs12664578	0.80[EUR][1000 genomes]
rs173333	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1753154	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1813847	0.80[EUR][1000 genomes]
rs1813848	0.80[EUR][1000 genomes]
rs183599	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1886751	0.80[EUR][1000 genomes]
rs1886752	0.80[EUR][1000 genomes]
rs1925688	0.80[EUR][1000 genomes]
rs1925695	0.80[EUR][1000 genomes]
rs2025630	0.80[EUR][1000 genomes]
rs2147920	0.80[EUR][1000 genomes]
rs2147921	0.80[EUR][1000 genomes]
rs2240459	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240460	0.82[ASN][1000 genomes]
rs242267	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242270	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242278	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242279	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242280	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242281	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242283	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs242285	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242286	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242287	0.91[EUR][1000 genomes]
rs2474349	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2985039	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs367353	0.82[AMR][1000 genomes]
rs369674	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734187	0.82[ASN][1000 genomes]
rs373646	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs376633	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812130	0.84[ASN][1000 genomes]
rs3812132	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs381782	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846773	0.82[ASN][1000 genomes]
rs3846774	0.82[ASN][1000 genomes]
rs3846775	0.82[ASN][1000 genomes]
rs3846776	0.82[ASN][1000 genomes]
rs3857485	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857488	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs390272	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3903920	0.81[EUR][1000 genomes]
rs3904088	0.81[EUR][1000 genomes]
rs395358	0.83[EUR][1000 genomes]
rs4110984	0.81[EUR][1000 genomes]
rs4110985	0.81[EUR][1000 genomes]
rs445434	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs446851	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs447077	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs448580	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs451089	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs451465	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451829	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4591818	0.82[ASN][1000 genomes]
rs4605853	0.80[EUR][1000 genomes]
rs4706289	0.80[EUR][1000 genomes]
rs4707346	0.80[EUR][1000 genomes]
rs4707347	0.81[EUR][1000 genomes]
rs4707351	0.80[EUR][1000 genomes]
rs4707352	0.80[EUR][1000 genomes]
rs4707356	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707357	0.84[ASN][1000 genomes]
rs4707358	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs499373	0.81[EUR][1000 genomes]
rs586771	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454591	0.80[EUR][1000 genomes]
rs6454592	0.80[EUR][1000 genomes]
rs6454595	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6454596	0.84[ASN][1000 genomes]
rs6454597	0.83[ASN][1000 genomes]
rs6454598	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454599	0.84[ASN][1000 genomes]
rs6454600	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6899394	0.84[ASN][1000 genomes]
rs6903219	0.80[EUR][1000 genomes]
rs6904310	0.80[EUR][1000 genomes]
rs6909021	0.80[EUR][1000 genomes]
rs6910991	0.82[ASN][1000 genomes]
rs6914193	0.80[EUR][1000 genomes]
rs6916994	0.84[ASN][1000 genomes]
rs6917432	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6921007	0.84[ASN][1000 genomes]
rs6921504	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6921619	0.80[EUR][1000 genomes]
rs6925648	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926831	0.83[EUR][1000 genomes]
rs6932678	0.82[ASN][1000 genomes]
rs6934603	0.84[ASN][1000 genomes]
rs6937874	0.84[ASN][1000 genomes]
rs6940544	0.84[ASN][1000 genomes]
rs7453986	0.84[ASN][1000 genomes]
rs7739034	0.80[EUR][1000 genomes]
rs7739726	0.80[EUR][1000 genomes]
rs7742478	0.80[EUR][1000 genomes]
rs7746545	0.81[EUR][1000 genomes]
rs7747129	0.80[EUR][1000 genomes]
rs7752485	0.80[EUR][1000 genomes]
rs7752882	0.81[EUR][1000 genomes]
rs7753030	0.84[ASN][1000 genomes]
rs7755244	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7757199	0.80[EUR][1000 genomes]
rs7758618	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7763365	0.80[EUR][1000 genomes]
rs7766324	0.80[EUR][1000 genomes]
rs7767449	0.80[EUR][1000 genomes]
rs7768575	0.80[EUR][1000 genomes]
rs7776407	0.80[EUR][1000 genomes]
rs910563	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294367	0.80[EUR][1000 genomes]
rs9294372	0.80[EUR][1000 genomes]
rs9344690	0.80[EUR][1000 genomes]
rs9344693	0.83[EUR][1000 genomes]
rs9344695	0.82[ASN][1000 genomes]
rs9344696	0.84[ASN][1000 genomes]
rs9344697	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9351117	0.80[EUR][1000 genomes]
rs9351124	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9353462	0.80[EUR][1000 genomes]
rs9353463	0.80[EUR][1000 genomes]
rs9353464	0.81[EUR][1000 genomes]
rs9353465	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9353468	0.83[ASN][1000 genomes]
rs9353473	0.84[ASN][1000 genomes]
rs9353483	0.80[EUR][1000 genomes]
rs9359743	0.84[ASN][1000 genomes]
rs9359748	0.80[EUR][1000 genomes]
rs9362408	0.80[EUR][1000 genomes]
rs9362415	0.83[ASN][1000 genomes]
rs9362417	0.84[ASN][1000 genomes]
rs9444479	0.80[EUR][1000 genomes]
rs9450647	0.84[ASN][1000 genomes]
rs9450650	0.84[ASN][1000 genomes]
rs9450652	0.84[ASN][1000 genomes]
rs994170	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv823771	chr6:88032762-88039447	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12190280	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs12190280	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs12190280	C6orf163	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88033000-88039600	Weak transcription	GM12878-XiMat	blood
2	chr6:88033000-88043600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:88033000-88043600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:88033000-88043600	Weak transcription	Spleen	Spleen
5	chr6:88033000-88049000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:88033000-88055200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:88033200-88042800	Weak transcription	Fetal Thymus	thymus
8	chr6:88033200-88043000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:88033200-88043400	Weak transcription	Primary T cells from cord blood	blood
10	chr6:88033200-88043600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:88033200-88043600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:88033200-88043600	Weak transcription	Pancreas	Pancrea
13	chr6:88033200-88045200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:88033200-88045400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:88033200-88048000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:88033200-88056400	Weak transcription	Liver	Liver
17	chr6:88033200-88062200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:88035800-88043400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:88038000-88038200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:88038000-88039000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:88038000-88039600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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