Variant report

Variant	rs6454630
Chromosome Location	chr6:88171357-88171358
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88171067..88173505-chr6:88175523..88178036,2	K562	blood:
2	chr6:88170826..88173711-chr6:88179114..88182210,3	K562	blood:
3	chr6:88118204..88120414-chr6:88170094..88172530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164414	Chromatin interaction
ENSG00000272514	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051131	0.82[CHB][hapmap]
rs1051148	0.82[CHB][hapmap]
rs10755484	0.82[CHB][hapmap]
rs13214153	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2103764	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2207144	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]
rs2207146	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2268993	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2268994	0.86[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273129	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2284908	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2300906	0.82[CHB][hapmap]
rs2300909	0.82[CHB][hapmap]
rs3757368	0.82[CHB][hapmap]
rs3918467	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs3934838	0.82[CHB][hapmap]
rs4334949	0.82[CHB][hapmap]
rs4464759	0.82[CHB][hapmap]
rs4587143	0.82[CHB][hapmap]
rs6903219	0.81[JPT][hapmap]
rs6905947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912958	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6914299	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916732	0.90[CHB][hapmap]
rs6933587	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7761814	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs7773906	0.82[CHB][hapmap]
rs9294379	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9294380	1.00[CEU][hapmap]
rs9294381	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9359748	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs9444504	0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444519	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs9444522	0.84[CHB][hapmap]
rs9450688	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450701	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450704	0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450712	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs9450723	0.82[CHB][hapmap]
rs9450732	0.82[CHB][hapmap]
rs9450752	0.82[CHB][hapmap]
rs985764	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6454630	C6orf162	cis	cerebellum	SCAN
rs6454630	C6orf164	cis	Thyroid	GTEx
rs6454630	C6orf162	cis	parietal	SCAN
rs6454630	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs6454630	C6orf165	cis	parietal	SCAN
rs6454630	SLC35A1	cis	multi-tissue	Pritchard
rs6454630	C6orf164	cis	lung	GTEx
rs6454630	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs6454630	SLC35A1	cis	parietal	SCAN
rs6454630	C6orf164	cis	Whole Blood	GTEx
rs6454630	SNORD50A	cis	cerebellum	SCAN
rs6454630	C6orf164	cis	multi-tissue	Pritchard
rs6454630	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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