Variant report

Variant	rs1125488
Chromosome Location	chr9:21481556-21481557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10491567	0.91[EUR][1000 genomes]
rs10811535	1.00[CEU][hapmap]
rs10811542	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10811545	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10811549	0.95[EUR][1000 genomes]
rs10811551	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10811556	0.91[EUR][1000 genomes]
rs10811562	0.84[EUR][1000 genomes]
rs10811563	0.84[EUR][1000 genomes]
rs10811564	0.82[EUR][1000 genomes]
rs10964981	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10964982	1.00[CEU][hapmap]
rs10964985	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs10964987	0.81[EUR][1000 genomes]
rs10964989	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10964998	0.88[AMR][1000 genomes]
rs10965002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs10965005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965008	1.00[CEU][hapmap]
rs10965010	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965029	0.84[EUR][1000 genomes]
rs10965031	0.93[EUR][1000 genomes]
rs10965034	0.98[EUR][1000 genomes]
rs10965036	0.98[EUR][1000 genomes]
rs10965050	0.80[EUR][1000 genomes]
rs10965053	0.84[EUR][1000 genomes]
rs10965054	0.84[EUR][1000 genomes]
rs10965059	0.88[EUR][1000 genomes]
rs10965063	0.82[EUR][1000 genomes]
rs11543888	0.82[EUR][1000 genomes]
rs12156640	1.00[CEU][hapmap]
rs12375583	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12376959	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377379	0.88[EUR][1000 genomes]
rs12378286	0.84[EUR][1000 genomes]
rs12378990	0.84[EUR][1000 genomes]
rs12379382	0.84[EUR][1000 genomes]
rs12379709	0.84[EUR][1000 genomes]
rs12379721	0.84[EUR][1000 genomes]
rs1332188	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16938384	1.00[CEU][hapmap]
rs16938433	0.98[EUR][1000 genomes]
rs16938435	0.93[EUR][1000 genomes]
rs16938448	0.84[EUR][1000 genomes]
rs2039380	0.91[EUR][1000 genomes]
rs2383190	0.86[AMR][1000 genomes]
rs55683539	0.84[EUR][1000 genomes]
rs55835613	0.88[EUR][1000 genomes]
rs55938615	0.86[EUR][1000 genomes]
rs56106002	0.85[ASN][1000 genomes]
rs56122777	0.88[EUR][1000 genomes]
rs56337511	0.98[EUR][1000 genomes]
rs7032680	0.91[EUR][1000 genomes]
rs7034161	1.00[CEU][hapmap]
rs72703410	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703411	0.93[EUR][1000 genomes]
rs72703417	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703418	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703419	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703426	0.98[EUR][1000 genomes]
rs72703445	0.88[EUR][1000 genomes]
rs72703447	0.84[EUR][1000 genomes]
rs72703449	0.84[EUR][1000 genomes]
rs72703450	0.84[EUR][1000 genomes]
rs7861480	0.85[CEU][hapmap]
rs9644855	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv466297	chr9:21391698-21507589	Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613758	chr9:21391698-21507589	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1030064	chr9:21455760-21524674	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	111 gene(s)	inside rSNPs	diseases
6	nsv613759	chr9:21455814-21492506	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1020445	chr9:21464962-21524162	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	109 gene(s)	inside rSNPs	diseases
8	nsv1020232	chr9:21464962-21524999	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
9	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
10	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
11	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
12	nsv525510	chr9:21481556-21484695	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21454800-21481600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:21463000-21502200	Weak transcription	HSMM	muscle
3	chr9:21466000-21527600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:21471600-21505600	Weak transcription	HUVEC	blood vessel
5	chr9:21475000-21485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:21477000-21505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:21477600-21482600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:21478800-21487200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:21479000-21481800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:21479600-21505000	Weak transcription	NHLF	lung
11	chr9:21480400-21481800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:21480600-21483000	Strong transcription	Osteobl	bone
13	chr9:21480600-21483200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:21481000-21481800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:21481000-21481800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:21481000-21481800	Strong transcription	NHDF-Ad	bronchial
17	chr9:21481000-21482000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:21481000-21482000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr9:21481000-21482000	Strong transcription	NH-A	brain
20	chr9:21481000-21482000	Strong transcription	NHEK	skin
21	chr9:21481000-21483200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr9:21481000-21483200	Strong transcription	HMEC	breast
23	chr9:21481200-21481600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:21481200-21481600	Strong transcription	A549	lung
25	chr9:21481200-21481800	Enhancers	Primary B cells from cord blood	blood
26	chr9:21481200-21481800	Enhancers	Gastric	stomach
27	chr9:21481200-21481800	Enhancers	Stomach Mucosa	stomach
28	chr9:21481200-21482000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr9:21481200-21482000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:21481400-21481600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:21481400-21481600	Enhancers	Primary hematopoietic stem cells	blood
32	chr9:21481400-21481800	Enhancers	Primary B cells from peripheral blood	blood
33	chr9:21481400-21481800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr9:21481400-21481800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:21481400-21482000	Enhancers	GM12878-XiMat	blood

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