Variant report

Variant	rs6473667
Chromosome Location	chr8:52840130-52840131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52829314..52832540-chr8:52837482..52840853,3	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10086425	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10094042	0.93[ASN][1000 genomes]
rs10101163	0.86[JPT][hapmap]
rs10105030	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1013621	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1013622	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11774370	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11781801	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11782727	0.86[ASN][1000 genomes]
rs11786818	0.94[ASN][1000 genomes]
rs11787499	0.86[JPT][hapmap]
rs12335014	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12677168	0.88[ASN][1000 genomes]
rs13252779	0.82[ASN][1000 genomes]
rs13252785	0.83[ASN][1000 genomes]
rs13256197	0.84[ASN][1000 genomes]
rs13263909	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13267241	0.91[ASN][1000 genomes]
rs13268494	0.82[ASN][1000 genomes]
rs13275077	0.84[ASN][1000 genomes]
rs13276858	0.93[ASN][1000 genomes]
rs13279123	0.82[ASN][1000 genomes]
rs1467197	0.94[ASN][1000 genomes]
rs1515688	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1517306	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1589079	0.86[EUR][1000 genomes]
rs16916858	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs16916952	0.85[JPT][hapmap]
rs2176121	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2395826	0.87[ASN][1000 genomes]
rs2395827	0.94[ASN][1000 genomes]
rs28619907	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34619309	0.84[ASN][1000 genomes]
rs35293585	0.85[ASN][1000 genomes]
rs4242474	0.82[ASN][1000 genomes]
rs4242475	0.82[ASN][1000 genomes]
rs4242476	0.82[ASN][1000 genomes]
rs4242479	0.86[JPT][hapmap]
rs4565453	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4873611	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6473660	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6473666	0.84[EUR][1000 genomes]
rs6982622	0.88[ASN][1000 genomes]
rs6983708	0.88[ASN][1000 genomes]
rs6986544	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6986984	0.90[CHB][hapmap]
rs6988122	0.88[ASN][1000 genomes]
rs6990379	0.82[ASN][1000 genomes]
rs6993367	0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7001651	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7004698	0.83[ASN][1000 genomes]
rs7013360	0.82[ASN][1000 genomes]
rs7017926	0.84[ASN][1000 genomes]
rs718251	0.82[ASN][1000 genomes]
rs722495	0.82[ASN][1000 genomes]
rs7461587	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7462096	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.84[ASN][1000 genomes]
rs7814421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7820177	0.85[EUR][1000 genomes]
rs7827298	0.91[ASN][1000 genomes]
rs7835856	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7843189	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs925762	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9298462	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[ASN][1000 genomes]

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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic 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 miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6473667	PCMTD1	cis	brain	seeQTL
rs6473667	PCMTD1	cis	cerebellum	SCAN
rs6473667	LOC115294	cis	multi-tissue	Pritchard
rs6473667	PCMTD1	trans	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52814200-52842000	Weak transcription	Brain Substantia Nigra	brain
2	chr8:52814200-52850000	Weak transcription	Spleen	Spleen
3	chr8:52815000-52852000	Weak transcription	Colon Smooth Muscle	Colon
4	chr8:52822600-52860200	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:52823000-52840200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr8:52831200-52840800	Weak transcription	Right Ventricle	heart
7	chr8:52831800-52841000	Weak transcription	Lung	lung
8	chr8:52831800-52858400	Weak transcription	Primary T cells from cord blood	blood
9	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
10	chr8:52835400-52840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr8:52837800-52851800	Weak transcription	Ovary	ovary
12	chr8:52838000-52840800	Weak transcription	Pancreas	Pancrea
13	chr8:52838000-52853400	Weak transcription	Esophagus	oesophagus
14	chr8:52838400-52840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr8:52838800-52842200	Enhancers	Left Ventricle	heart
16	chr8:52839200-52841000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr8:52839600-52840600	Weak transcription	Psoas Muscle	Psoas

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