Variant report

Variant	rs9342112
Chromosome Location	chr6:88092491-88092492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf164-2	chr6:88091867-88096525	NONHSAT113901

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1051550	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11964237	0.80[CHD][hapmap];0.87[TSI][hapmap]
rs1203155	0.90[ASN][1000 genomes]
rs1203156	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1209113	0.91[ASN][1000 genomes]
rs12529410	0.80[CHD][hapmap];0.85[TSI][hapmap]
rs12529423	0.85[TSI][hapmap]
rs12661245	0.81[ASN][1000 genomes]
rs12663865	1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13217485	0.80[CHD][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap]
rs173334	0.91[ASN][1000 genomes]
rs1884320	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs242271	0.92[ASN][1000 genomes]
rs242272	0.92[ASN][1000 genomes]
rs242273	0.87[ASN][1000 genomes]
rs242291	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs242292	0.90[ASN][1000 genomes]
rs242293	0.90[ASN][1000 genomes]
rs34977536	0.80[AMR][1000 genomes]
rs3736740	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs406900	0.92[ASN][1000 genomes]
rs414013	0.92[ASN][1000 genomes]
rs4329082	0.81[ASN][1000 genomes]
rs4707365	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707367	1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707368	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707369	0.85[ASN][1000 genomes]
rs4707370	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4707371	0.83[ASN][1000 genomes]
rs4707372	0.83[ASN][1000 genomes]
rs6454611	0.81[ASN][1000 genomes]
rs6454612	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6454613	0.81[ASN][1000 genomes]
rs6454615	0.81[ASN][1000 genomes]
rs6454616	0.80[CHD][hapmap];0.84[TSI][hapmap]
rs6454618	0.89[ASW][hapmap];0.80[CHD][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs6454622	0.82[YRI][hapmap]
rs6454623	0.89[YRI][hapmap]
rs6454624	0.83[YRI][hapmap]
rs6454625	0.80[CHD][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap]
rs6454626	0.83[YRI][hapmap]
rs6900397	0.80[CHD][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap]
rs6906433	0.85[AMR][1000 genomes]
rs6907825	1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6910429	0.80[CHD][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs6912282	0.90[CEU][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6915562	0.80[CHD][hapmap];0.85[TSI][hapmap]
rs6919775	0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs6920937	0.81[ASN][1000 genomes]
rs6930072	0.81[ASN][1000 genomes]
rs6930076	0.92[ASN][1000 genomes]
rs6940716	0.80[CHD][hapmap]
rs694524	0.92[ASN][1000 genomes]
rs7744338	0.83[CEU][hapmap];0.80[CHD][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7744793	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746876	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7749047	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7749162	0.81[ASN][1000 genomes]
rs7753821	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7760108	0.81[ASN][1000 genomes]
rs7761462	0.83[ASN][1000 genomes]
rs7764266	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7764963	1.00[CEU][hapmap]
rs7766462	0.81[ASN][1000 genomes]
rs7767220	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7773262	0.81[ASN][1000 genomes]
rs7773804	0.81[ASN][1000 genomes]
rs926946	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9294377	0.92[ASN][1000 genomes]
rs9294378	0.83[ASN][1000 genomes]
rs9344708	0.83[ASN][1000 genomes]
rs9353484	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9353486	0.83[ASN][1000 genomes]
rs9353487	0.83[ASN][1000 genomes]
rs9353488	0.83[ASN][1000 genomes]
rs9362426	0.94[ASN][1000 genomes]
rs9362428	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9444493	0.81[ASN][1000 genomes]
rs9450662	0.92[ASN][1000 genomes]
rs9450682	0.80[CHD][hapmap]

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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9342112	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9342112	C6orf164	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88061600-88094600	Weak transcription	Left Ventricle	heart
4	chr6:88080200-88093800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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