Variant report

Variant	rs6727017
Chromosome Location	chr2:172766847-172766848
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172764440..172768356-chr2:172769175..172774540,8	K562	blood:
2	chr2:172763759..172768235-chr2:172769175..172774540,7	K562	blood:
3	chr2:172764720..172767665-chr2:172778015..172780432,2	K562	blood:
4	chr2:172763906..172767065-chr2:172777773..172780432,4	K562	blood:
5	chr2:172750354..172753126-chr2:172762746..172766983,5	MCF-7	breast:
6	chr2:172765258..172766911-chr2:172774816..172776433,2	K562	blood:

Variant related genes	Relation type
ENSG00000128708	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10165126	0.83[CEU][hapmap]
rs10166548	0.81[AMR][1000 genomes]
rs10167419	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs10174055	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs10194102	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs10200608	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs10201430	0.83[EUR][1000 genomes]
rs10202823	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206062	0.82[CEU][hapmap];0.93[JPT][hapmap]
rs10207085	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs10930502	0.83[CEU][hapmap]
rs11757	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs11904009	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs12692973	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs12692974	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs13030911	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165934	0.83[EUR][1000 genomes]
rs2292815	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs312918	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs3770445	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs3770451	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs3770452	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs4667694	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs4668414	0.83[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs62182433	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6433319	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6710698	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs6715929	0.92[CEU][hapmap]
rs6722757	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs6724337	0.83[CEU][hapmap]
rs6725388	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs6731562	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6745143	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs6750058	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6752812	0.88[CEU][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs6754817	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs6758704	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs6759575	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs7563971	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564089	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573003	0.84[CEU][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs7581072	0.82[AMR][1000 genomes]
rs7586207	0.83[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs7597387	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7602037	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7608403	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs908670	0.93[JPT][hapmap]
rs908671	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs973889	0.84[CEU][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6727017	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6727017	AC068039.4	cis	Thyroid	GTEx
rs6727017	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6727017	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6727017	AC068039.4	cis	Whole Blood	GTEx
rs6727017	AC068039.4	cis	Stomach	GTEx
rs6727017	AC068039.4	cis	Muscle Skeletal	GTEx
rs6727017	SLC25A12	cis	multi-tissue	Pritchard
rs6727017	AC068039.4	cis	Nerve Tibial	GTEx
rs6727017	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6727017	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6727017	AC068039.4	cis	lung	GTEx

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

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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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