Variant report

Variant	rs12913397
Chromosome Location	chr15:31296852-31296853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31281475..31285433-chr15:31293926..31297603,3	K562	blood:
2	chr15:31283942..31285617-chr15:31294497..31297263,2	MCF-7	breast:
3	chr15:31282443..31284483-chr15:31294719..31297603,2	K562	blood:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11070718	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133642	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11638295	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12439664	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12443369	0.83[ASN][1000 genomes]
rs12901022	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905872	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12914207	0.88[ASN][1000 genomes]
rs12914438	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1404468	0.88[ASN][1000 genomes]
rs1404469	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1404470	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1425291	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1524876	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1880499	0.91[ASN][1000 genomes]
rs2113946	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28564430	0.94[ASN][1000 genomes]
rs2949569	0.81[ASN][1000 genomes]
rs2949570	0.81[ASN][1000 genomes]
rs2949571	0.81[ASN][1000 genomes]
rs2949573	0.88[ASN][1000 genomes]
rs2949577	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2955783	0.91[ASN][1000 genomes]
rs2955790	0.81[ASN][1000 genomes]
rs2959049	0.91[ASN][1000 genomes]
rs3743231	0.82[ASN][1000 genomes]
rs3743233	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4344701	0.88[ASN][1000 genomes]
rs58083498	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493387	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493388	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164939	0.88[ASN][1000 genomes]
rs7170710	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7175967	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8040989	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964925	0.95[ASN][1000 genomes]

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	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:34 , 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	chr15:31293600-31298400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:31294600-31298600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:31295600-31297200	Enhancers	Spleen	Spleen
5	chr15:31295600-31297800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:31295800-31297200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr15:31296000-31297200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:31296000-31298000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr15:31296000-31298200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:31296200-31297000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:31296200-31297000	Enhancers	Primary T cells from cord blood	blood
12	chr15:31296200-31297000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:31296200-31297000	Enhancers	Adipose Nuclei	Adipose
14	chr15:31296200-31297000	Flanking Active TSS	GM12878-XiMat	blood
15	chr15:31296200-31297000	Enhancers	HMEC	breast
16	chr15:31296200-31297200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr15:31296200-31297200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:31296200-31297800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:31296400-31297200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:31296400-31298200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:31296600-31297000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:31296600-31298000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:31296600-31299000	Enhancers	Primary B cells from cord blood	blood
24	chr15:31296600-31299000	Enhancers	Primary B cells from peripheral blood	blood
25	chr15:31296600-31304200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:31296800-31297000	Flanking Active TSS	HUVEC	blood vessel
27	chr15:31296800-31297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:31296800-31297600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:31296800-31297800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:31296800-31297800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:31296800-31297800	Enhancers	Primary hematopoietic stem cells	blood
32	chr15:31296800-31298200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr15:31296800-31300200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:31296800-31306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links