Variant report

Variant	rs9534966
Chromosome Location	chr13:48711678-48711679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs12869161	0.96[AMR][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs1327656	0.96[AMR][1000 genomes]
rs1359616	0.87[AMR][1000 genomes]
rs1410116	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs1752129	0.83[AMR][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1927214	0.96[AMR][1000 genomes]
rs1998988	0.83[AMR][1000 genomes]
rs1998989	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025864	0.96[AMR][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs2094193	0.96[AMR][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2148939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148940	0.96[AMR][1000 genomes]
rs2182373	0.96[AMR][1000 genomes]
rs2182375	1.00[MEX][hapmap]
rs2182378	0.87[AMR][1000 genomes]
rs2182785	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs2406796	0.96[AMR][1000 genomes]
rs2406798	0.96[AMR][1000 genomes]
rs2765077	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3862747	0.83[AMR][1000 genomes]
rs3990876	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4427704	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4941618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs4942723	0.83[AMR][1000 genomes]
rs4942724	0.87[AMR][1000 genomes]
rs4942732	0.87[AMR][1000 genomes]
rs4942734	0.87[AMR][1000 genomes]
rs4942736	0.87[AMR][1000 genomes]
rs4942740	0.96[AMR][1000 genomes]
rs4942746	0.96[AMR][1000 genomes]
rs61973264	0.91[AMR][1000 genomes]
rs61973265	0.83[AMR][1000 genomes]
rs61973266	0.87[AMR][1000 genomes]
rs61973307	0.83[AMR][1000 genomes]
rs61973308	0.83[AMR][1000 genomes]
rs61974562	0.87[AMR][1000 genomes]
rs61974579	0.87[AMR][1000 genomes]
rs6561426	0.87[AMR][1000 genomes]
rs6561438	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7317685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323702	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs7324368	0.83[AMR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs7326381	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7326418	0.83[AMR][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs7329615	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs7332363	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs7332994	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs7335797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes]
rs7336170	0.96[AMR][1000 genomes]
rs73481288	0.96[ASN][1000 genomes]
rs73483108	0.96[ASN][1000 genomes]
rs73483122	0.96[ASN][1000 genomes]
rs7985469	0.96[AMR][1000 genomes]
rs7990099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs7990541	0.87[AMR][1000 genomes]
rs7991892	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs7996581	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs7997347	0.82[MEX][hapmap]
rs7998786	0.87[AMR][1000 genomes]
rs7999270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs8001509	0.87[AMR][1000 genomes]
rs8002322	0.90[MEX][hapmap]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs840428	0.83[AMR][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs840435	0.87[AMR][1000 genomes]
rs840437	0.83[AMR][1000 genomes]
rs840439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9316350	0.96[AMR][1000 genomes]
rs9316351	0.96[AMR][1000 genomes]
rs943066	0.83[AMR][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9526431	0.87[AMR][1000 genomes]
rs9526441	0.84[AMR][1000 genomes]
rs9526448	0.96[AMR][1000 genomes]
rs9526450	1.00[ASN][1000 genomes]
rs9526454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9534956	0.96[AMR][1000 genomes]
rs9534959	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562792	0.87[AMR][1000 genomes]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9534966	MED4	cis	uninvolved skin	skin_eQTL
rs9534966	MED4	cis	cerebellum	SCAN
rs9534966	MED4	cis	multi-tissue	Pritchard
rs9534966	SUCLA2	cis	multi-tissue	Pritchard
rs9534966	MED4	cis	lesional skin	skin_eQTL
rs9534966	FAM194B	cis	cerebellum	SCAN
rs9534966	MED4	cis	normal skin	skin_eQTL
rs9534966	MED4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48701800-48725800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:48702200-48713800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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