Variant report

Variant	rs1706829
Chromosome Location	chr15:45514150-45514151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45478493..45480559-chr15:45513673..45516315,2	MCF-7	breast:
2	chr15:45512789..45515700-chr15:45518992..45521212,2	MCF-7	breast:
3	chr15:45489158..45491324-chr15:45514071..45516738,2	K562	blood:

Variant related genes	Relation type
ENSG00000138606	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10519018	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs1060896	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs1145089	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11632752	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs11632778	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs11632920	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs11637838	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs11637920	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs11639420	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs12904150	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs12908818	1.00[CHD][hapmap]
rs12915314	0.87[YRI][hapmap]
rs1620253	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs1648304	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1648307	1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs1648308	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1648312	1.00[JPT][hapmap]
rs1648317	1.00[JPT][hapmap]
rs1648318	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1706808	1.00[JPT][hapmap]
rs1706813	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1706817	0.82[AMR][1000 genomes]
rs1706820	1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs1706826	1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1706827	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1719250	1.00[CHD][hapmap]
rs2162246	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs2413768	0.85[CHD][hapmap];0.87[YRI][hapmap]
rs2413772	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs2413774	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs2458237	0.82[AMR][1000 genomes]
rs2461705	1.00[CHD][hapmap]
rs2467819	0.82[AMR][1000 genomes]
rs2467820	0.82[AMR][1000 genomes]
rs28851313	1.00[ASN][1000 genomes]
rs4775830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs6493144	0.92[CHD][hapmap]
rs7167146	1.00[CHD][hapmap]
rs7169193	1.00[JPT][hapmap]
rs8024620	0.92[CHD][hapmap]
rs8039138	0.87[YRI][hapmap]
rs8039352	1.00[CHD][hapmap]
rs8039354	1.00[CHD][hapmap];0.87[YRI][hapmap]
rs8039540	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv977712	chr15:45501081-45515127	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1706829	SHF	cis	cerebellum	SCAN
rs1706829	SHF	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45510400-45516800	Weak transcription	Pancreas	Pancrea
2	chr15:45510800-45514200	Weak transcription	Fetal Intestine Large	intestine
3	chr15:45514000-45514200	Enhancers	Stomach Mucosa	stomach

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