Variant report

Variant	rs9444490
Chromosome Location	chr6:87977841-87977842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1145713	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145714	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145715	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145716	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11759727	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188806	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1188816	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1188817	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1188818	0.81[ASN][1000 genomes]
rs1188819	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1203162	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203163	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203164	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12194354	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12211627	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13201289	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1630494	0.82[ASN][1000 genomes]
rs16878497	0.85[EUR][1000 genomes]
rs1739886	0.81[ASN][1000 genomes]
rs1746444	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1753152	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1753159	0.82[ASN][1000 genomes]
rs181491	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925686	0.85[EUR][1000 genomes]
rs2236048	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2257153	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs242264	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs242265	0.82[ASN][1000 genomes]
rs242266	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs242268	0.82[ASN][1000 genomes]
rs242269	0.82[ASN][1000 genomes]
rs242274	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs242275	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs242276	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs242277	0.83[ASN][1000 genomes]
rs242282	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2983136	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs368267	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs374792	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs377288	0.81[AMR][1000 genomes]
rs379455	0.83[ASN][1000 genomes]
rs381741	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs381798	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs382956	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs383692	0.81[ASN][1000 genomes]
rs384318	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs385210	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3857486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs392807	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs398140	0.81[ASN][1000 genomes]
rs3999791	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406981	0.81[ASN][1000 genomes]
rs411606	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413687	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs414453	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235830	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs452315	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4707344	0.85[EUR][1000 genomes]
rs4707345	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4707355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs490447	0.82[ASN][1000 genomes]
rs540975	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs541170	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6908834	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913159	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6921673	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926686	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6932641	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6938885	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6939075	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940325	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7752414	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757330	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs827433	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910564	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs910565	0.82[ASN][1000 genomes]
rs912815	0.86[EUR][1000 genomes]
rs9294375	0.84[EUR][1000 genomes]
rs9294376	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444476	0.84[EUR][1000 genomes]
rs9444481	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444486	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444491	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450623	0.85[EUR][1000 genomes]
rs9450630	0.86[EUR][1000 genomes]
rs9450636	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450637	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450638	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450639	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450640	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450651	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450653	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9444490	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9444490	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9444490	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444490	C6orf162	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87957200-87981000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:87966400-87989200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:87967600-87983000	Weak transcription	Esophagus	oesophagus
4	chr6:87967800-87989000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:87968200-87991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:87968400-87984400	Weak transcription	NHDF-Ad	bronchial
7	chr6:87968600-87984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:87969800-87981800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:87970000-87984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:87970200-87978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:87970200-87984600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:87970400-87978000	Weak transcription	Left Ventricle	heart
13	chr6:87970400-87984400	Weak transcription	NH-A	brain
14	chr6:87970600-87983400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:87970600-87984200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:87970600-87988800	Weak transcription	Fetal Thymus	thymus
17	chr6:87970600-87994800	Weak transcription	Fetal Brain Female	brain
18	chr6:87971200-87985800	Weak transcription	Brain Germinal Matrix	brain
19	chr6:87974800-87978600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:87975000-87984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:87975200-87982200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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