Variant report

Variant	rs2207144
Chromosome Location	chr6:88150816-88150817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1051131	0.91[CHB][hapmap]
rs1051148	0.91[CHB][hapmap];0.84[GIH][hapmap]
rs10755484	0.91[CHB][hapmap];0.84[GIH][hapmap]
rs107690	0.90[MEX][hapmap]
rs1188816	0.83[CHB][hapmap]
rs13214153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1753153	0.80[MEX][hapmap]
rs2103764	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207146	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs2268993	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs2268994	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs2273129	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs2284908	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2300906	0.91[CHB][hapmap]
rs2300909	0.91[CHB][hapmap]
rs242267	0.80[MEX][hapmap]
rs242270	0.90[MEX][hapmap]
rs242287	0.90[MEX][hapmap]
rs369674	0.85[MEX][hapmap]
rs373646	0.90[MEX][hapmap]
rs3757368	0.91[CHB][hapmap];0.84[GIH][hapmap]
rs3918467	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap]
rs3934838	0.91[CHB][hapmap]
rs4334949	0.91[CHB][hapmap];0.84[GIH][hapmap]
rs4464759	0.91[CHB][hapmap];0.84[GIH][hapmap]
rs448580	0.81[MEX][hapmap]
rs451465	0.85[MEX][hapmap]
rs4587143	0.91[CHB][hapmap]
rs6454630	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454631	0.86[CHB][hapmap]
rs6903219	0.86[JPT][hapmap]
rs6905947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912958	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916732	0.95[CHB][hapmap]
rs6933587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7741825	0.81[CHB][hapmap]
rs7761814	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7773906	0.91[CHB][hapmap]
rs910563	0.85[MEX][hapmap]
rs9294379	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294380	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs9294381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359748	0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs9444504	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs9444519	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs9444522	0.89[CHB][hapmap]
rs9450688	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450704	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs9450712	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9450723	0.91[CHB][hapmap]
rs9450732	0.91[CHB][hapmap]
rs9450752	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs985764	0.91[CHB][hapmap]

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	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
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2207144	C6orf164	cis	Esophagus Muscularis	GTEx
rs2207144	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2207144	C6orf164	cis	lung	GTEx
rs2207144	SLC35A1	cis	multi-tissue	Pritchard
rs2207144	C6orf164	cis	Thyroid	GTEx
rs2207144	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs2207144	C6orf165	cis	parietal	SCAN
rs2207144	C6orf164	cis	Whole Blood	GTEx
rs2207144	C6orf162	cis	cerebellum	SCAN
rs2207144	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx
rs2207144	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2207144	SLC35A1	cis	lymphoblastoid	seeQTL
rs2207144	C6orf162	cis	parietal	SCAN
rs2207144	SNORD50A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88150000-88154400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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