Variant report

Variant	rs12901022
Chromosome Location	chr15:31312743-31312744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10163148	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11070678	0.92[CHB][hapmap]
rs11070718	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133642	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11638295	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12439664	0.89[ASN][1000 genomes]
rs12441318	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12443369	0.81[ASN][1000 genomes]
rs12905872	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913397	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12914207	0.86[ASN][1000 genomes]
rs12914438	0.89[ASN][1000 genomes]
rs1404468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1404469	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1404470	0.89[ASN][1000 genomes]
rs1425291	0.89[ASN][1000 genomes]
rs1474381	0.92[CHB][hapmap]
rs1474382	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1524876	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs1880499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2042613	1.00[CHB][hapmap]
rs2113945	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2113946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272218	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2272219	0.92[CHB][hapmap]
rs2293314	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2293319	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2293320	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs28564430	0.92[ASN][1000 genomes]
rs28693590	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2873	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2949569	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2949570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2949573	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs2949575	0.92[CHB][hapmap]
rs2949576	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2949577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2949578	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2955783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2955787	0.92[CHB][hapmap]
rs2955790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2955791	0.92[CHB][hapmap]
rs2955796	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2959039	0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2959049	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs3743231	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs3743233	0.92[ASN][1000 genomes]
rs4344701	0.89[ASN][1000 genomes]
rs4779796	0.92[CHB][hapmap]
rs4779797	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs58083498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493387	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161812	0.92[CHB][hapmap]
rs7164939	0.89[ASN][1000 genomes]
rs7165798	1.00[CHB][hapmap]
rs7169064	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs7170710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7175951	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs7175967	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176351	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs7178375	0.92[CHB][hapmap]
rs7178533	0.92[CHB][hapmap]
rs7182143	1.00[CHB][hapmap]
rs8040989	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8041717	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs964925	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9806159	0.92[CHB][hapmap];0.83[CHD][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	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12901022	RP11-540B6.3	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31305000-31314800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:31307200-31315800	Weak transcription	HepG2	liver
3	chr15:31307400-31313000	Weak transcription	GM12878-XiMat	blood
4	chr15:31307800-31312800	Weak transcription	Primary B cells from cord blood	blood
5	chr15:31308000-31314000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:31309000-31314400	Weak transcription	HUVEC	blood vessel
7	chr15:31309200-31313400	Weak transcription	Placenta	Placenta
8	chr15:31309800-31314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:31310000-31314600	Weak transcription	NHEK	skin
10	chr15:31310000-31315200	Weak transcription	Fetal Kidney	kidney
11	chr15:31310200-31315200	Weak transcription	NHLF	lung
12	chr15:31310400-31315000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:31311000-31319600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:31312000-31315800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:31312200-31313200	Enhancers	Stomach Mucosa	stomach
16	chr15:31312400-31312800	Enhancers	Gastric	stomach
17	chr15:31312400-31313200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:31312400-31317400	Enhancers	Primary B cells from peripheral blood	blood
19	chr15:31312600-31313000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:31312600-31313400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:31312600-31313400	Enhancers	Osteobl	bone

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