Variant report

Variant	rs7747129
Chromosome Location	chr6:88090295-88090296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs107689	0.86[EUR][1000 genomes]
rs107690	0.86[EUR][1000 genomes]
rs1201409	0.85[EUR][1000 genomes]
rs12190280	0.80[EUR][1000 genomes]
rs12207825	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs173333	0.84[EUR][1000 genomes]
rs1753154	0.80[EUR][1000 genomes]
rs183599	0.85[EUR][1000 genomes]
rs242267	0.86[EUR][1000 genomes]
rs242270	0.86[EUR][1000 genomes]
rs242278	0.83[EUR][1000 genomes]
rs242279	0.84[EUR][1000 genomes]
rs242280	0.84[EUR][1000 genomes]
rs242281	0.84[EUR][1000 genomes]
rs242285	0.86[EUR][1000 genomes]
rs242286	0.86[EUR][1000 genomes]
rs242287	0.86[EUR][1000 genomes]
rs2474349	0.81[EUR][1000 genomes]
rs2985039	0.83[EUR][1000 genomes]
rs369674	0.84[EUR][1000 genomes]
rs373646	0.85[EUR][1000 genomes]
rs376633	0.84[EUR][1000 genomes]
rs381782	0.84[EUR][1000 genomes]
rs390272	0.81[EUR][1000 genomes]
rs445434	0.82[EUR][1000 genomes]
rs446851	0.84[EUR][1000 genomes]
rs447077	0.84[EUR][1000 genomes]
rs448580	0.84[EUR][1000 genomes]
rs451089	0.83[EUR][1000 genomes]
rs451465	0.84[EUR][1000 genomes]
rs451829	0.84[EUR][1000 genomes]
rs586771	0.86[EUR][1000 genomes]
rs6903219	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921504	0.85[EUR][1000 genomes]
rs7746545	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910563	0.85[EUR][1000 genomes]
rs9353483	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9359748	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9359749	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9362427	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7747129	C6orf164	cis	Esophagus Muscularis	GTEx
rs7747129	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs7747129	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs7747129	C6orf164	cis	Thyroid	GTEx
rs7747129	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs7747129	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs7747129	C6orf164	cis	Whole Blood	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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