Variant report

Variant	rs1706799
Chromosome Location	chr15:45618234-45618235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45618068..45621041-chr15:45630551..45632490,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10152337	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10152697	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10851425	0.86[CHB][hapmap]
rs1145073	0.80[LWK][hapmap]
rs12324848	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1288861	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1288863	0.86[CHB][hapmap]
rs1288865	0.86[CHB][hapmap]
rs16940351	0.91[JPT][hapmap];0.81[TSI][hapmap]
rs16941238	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs16942066	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17533116	0.93[EUR][1000 genomes]
rs17533716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535381	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17537244	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17618294	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2433229	0.83[JPT][hapmap]
rs2433602	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2433605	0.80[LWK][hapmap]
rs2453546	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2461706	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2467857	0.80[LWK][hapmap]
rs2486287	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2486289	0.80[LWK][hapmap]
rs2668746	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55721266	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55904415	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56267974	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56273246	0.85[ASN][1000 genomes]
rs56306977	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56327050	0.85[ASN][1000 genomes]
rs56937414	0.83[ASN][1000 genomes]
rs56967490	0.85[ASN][1000 genomes]
rs57369693	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57419781	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61301536	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72709081	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72709084	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72709088	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72711253	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72711255	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72711259	0.85[ASN][1000 genomes]
rs9972405	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972498	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972528	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv977713	chr15:45611707-45620772	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1706799	MGA	cis	parietal	SCAN
rs1706799	SLC28A2	cis	cerebellum	SCAN
rs1706799	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1706799	SLC30A4	cis	parietal	SCAN
rs1706799	RPAP1	cis	cerebellum	SCAN
rs1706799	SPATA5L1	cis	multi-tissue	Pritchard
rs1706799	ITPKA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45613600-45622000	Weak transcription	Pancreas	Pancrea
2	chr15:45614200-45619000	Weak transcription	Fetal Brain Female	brain
3	chr15:45616000-45624800	Weak transcription	Gastric	stomach
4	chr15:45616200-45618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:45616200-45625000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:45616200-45625600	Weak transcription	Fetal Intestine Small	intestine
7	chr15:45617200-45618800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:45617200-45621200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr15:45617600-45618800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr15:45617800-45621600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:45618000-45618600	Enhancers	Brain Hippocampus Middle	brain
12	chr15:45618000-45618800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:45618000-45619000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:45618000-45619400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr15:45618200-45619600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:45618200-45619600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:45618200-45619600	Enhancers	Fetal Brain Male	brain

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