Variant report

Variant	rs10965002
Chromosome Location	chr9:21455814-21455815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFNE-1	chr9:21455641-21455943	ENSG00000171889
2	lnc-IFNE-1	chr9:21454267-21455943	NONHSAT130385
3	lnc-IFNE-1	chr9:21454267-21455943	NONHSAT130386
4	lnc-IFNE-1	chr9:21455587-21455943	NONHSAT130388
5	lnc-IFNA1-1	chr9:21455483-21456048	NONHSAT130387

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10811535	1.00[CEU][hapmap]
rs10811542	0.88[EUR][1000 genomes]
rs10811545	0.88[EUR][1000 genomes]
rs10811551	1.00[CEU][hapmap]
rs10964981	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs10964982	1.00[CEU][hapmap]
rs10964985	1.00[CEU][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs10964986	0.80[EUR][1000 genomes]
rs10964987	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10964989	0.88[EUR][1000 genomes]
rs10964998	0.97[EUR][1000 genomes]
rs10965005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965008	1.00[CEU][hapmap]
rs10965010	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965034	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10965036	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1125488	0.85[ASN][1000 genomes]
rs12156640	1.00[CEU][hapmap]
rs12375583	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12376959	0.85[ASN][1000 genomes]
rs12377379	0.82[AMR][1000 genomes]
rs1332188	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16938384	1.00[CEU][hapmap]
rs16938433	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2383190	0.95[EUR][1000 genomes]
rs55938615	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56106002	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56122777	0.90[AMR][1000 genomes]
rs56337511	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7034161	1.00[CEU][hapmap]
rs72703410	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72703417	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72703418	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72703419	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72703426	0.81[EUR][1000 genomes]
rs72703445	0.86[AMR][1000 genomes]
rs7861480	0.85[CEU][hapmap]
rs7867089	0.83[EUR][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	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	nsv892739	chr9:21407250-21470520	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21451400-21458800	Weak transcription	A549	lung
2	chr9:21451800-21457600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:21453200-21456200	Strong transcription	NH-A	brain
4	chr9:21453800-21456000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:21454400-21456200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:21454800-21474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:21454800-21481600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:21455000-21456800	Weak transcription	Hela-S3	cervix
9	chr9:21455000-21457200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:21455200-21456000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:21455200-21456000	Genic enhancers	NHEK	skin
12	chr9:21455200-21457200	Strong transcription	Osteobl	bone
13	chr9:21455200-21464000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:21455200-21481000	Weak transcription	NHDF-Ad	bronchial
15	chr9:21455400-21456000	Strong transcription	HMEC	breast
16	chr9:21455400-21456400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr9:21455400-21462600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:21455600-21456000	Genic enhancers	NHLF	lung
19	chr9:21455800-21456000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:21455800-21457000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:21455800-21481000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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