Variant report

Variant	rs964925
Chromosome Location	chr15:31305979-31305980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10519726	0.91[CHB][hapmap]
rs11070718	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1133642	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11638295	0.84[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12439664	0.89[ASN][1000 genomes]
rs12441318	1.00[JPT][hapmap]
rs12442333	0.90[CHB][hapmap]
rs12901022	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12905872	0.97[ASN][1000 genomes]
rs12913397	0.95[ASN][1000 genomes]
rs12914207	0.83[ASN][1000 genomes]
rs12914438	0.89[ASN][1000 genomes]
rs1404468	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1404469	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1404470	0.89[ASN][1000 genomes]
rs1425291	0.89[ASN][1000 genomes]
rs1524876	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16956341	0.91[CHB][hapmap]
rs16956362	0.91[CHB][hapmap]
rs16956366	0.91[CHB][hapmap]
rs16956414	0.91[CHB][hapmap]
rs16956422	0.91[CHB][hapmap]
rs1880499	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2042613	0.84[CHB][hapmap]
rs2113945	0.83[CHD][hapmap]
rs2113946	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2272218	0.84[CHD][hapmap]
rs2293314	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2293320	0.84[CHD][hapmap]
rs28564430	0.89[ASN][1000 genomes]
rs2873	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2949569	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2949570	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2949573	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2949576	0.84[CHD][hapmap]
rs2949577	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2949578	0.84[CHD][hapmap]
rs2955783	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2955790	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2955796	0.90[JPT][hapmap]
rs2959039	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2959049	0.89[ASN][1000 genomes]
rs3743231	0.84[CHD][hapmap]
rs3743233	0.89[ASN][1000 genomes]
rs3784588	0.91[CHB][hapmap]
rs4344701	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58083498	0.97[ASN][1000 genomes]
rs6493358	0.91[CHB][hapmap]
rs6493387	0.97[ASN][1000 genomes]
rs6493388	0.97[ASN][1000 genomes]
rs7164939	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165798	0.83[CHB][hapmap]
rs7170710	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7175354	0.81[CHB][hapmap]
rs7175951	0.84[CHD][hapmap]
rs7175967	0.91[ASN][1000 genomes]
rs7182143	0.83[CHB][hapmap]
rs8040989	0.84[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8041717	0.84[CHD][hapmap]
rs871312	0.91[CHB][hapmap]
rs872843	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats 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
7	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	esv2760394	chr15:31297865-31306229	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs964925	RP11-540B6.3	cis	lung	GTEx
rs964925	GABRB3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31291800-31308000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:31296800-31306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:31299000-31308800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:31304600-31307600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:31305000-31314800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:31305200-31306200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:31305200-31308200	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:31305200-31309200	Enhancers	Placenta	Placenta
9	chr15:31305400-31306800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:31305600-31306000	Enhancers	Primary T cells from cord blood	blood
11	chr15:31305600-31307200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr15:31305600-31307800	Enhancers	Primary B cells from cord blood	blood
13	chr15:31305800-31306000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr15:31305800-31306200	Enhancers	Liver	Liver
15	chr15:31305800-31306400	Enhancers	HepG2	liver
16	chr15:31305800-31307000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:31305800-31307000	Flanking Active TSS	GM12878-XiMat	blood
18	chr15:31305800-31307200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr15:31305800-31308000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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