Variant report

Variant	rs10429330
Chromosome Location	chr8:68453664-68453665
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	chr8:68452723..68454927-chr8:68489405..68492121,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10429329	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957390	0.81[JPT][hapmap]
rs10957391	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs11785565	0.81[JPT][hapmap]
rs13262307	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13262388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933366	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1818154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818155	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818156	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948823	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2047833	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs2134598	0.96[ASN][1000 genomes]
rs2380414	1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs2380415	0.81[JPT][hapmap]
rs2380416	0.81[JPT][hapmap]
rs4737239	0.81[JPT][hapmap]
rs4737840	0.95[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4737843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737844	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737845	0.95[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6472317	0.95[CEU][hapmap]
rs7000339	0.94[EUR][1000 genomes]
rs7002272	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7017892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7017897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7824497	0.84[CEU][hapmap]
rs7831538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs924740	0.90[JPT][hapmap]
rs924741	0.90[JPT][hapmap]
rs924742	0.82[CHB][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	esv2752263	chr8:68170946-68788493	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024135	chr8:68235792-68629789	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
3	nsv539642	chr8:68235792-68629789	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752264	chr8:68244546-68647201	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10429330	PLOD2	trans	parietal	SCAN
rs10429330	PTTG3P	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:68451600-68454400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr8:68452000-68454400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr8:68452000-68454600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr8:68452200-68454600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:68452800-68454000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr8:68452800-68454200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr8:68452800-68459000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:68453000-68454200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr8:68453000-68454600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr8:68453400-68453800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr8:68453400-68453800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr8:68453600-68453800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr8:68453600-68453800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr8:68453600-68454200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:68453600-68456800	Weak transcription	Dnd41	blood

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