Variant report

Variant	rs2399334
Chromosome Location	chr3:110301025-110301026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1022206	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1154944	0.86[EUR][1000 genomes]
rs11714695	0.86[EUR][1000 genomes]
rs11718338	0.86[EUR][1000 genomes]
rs12489421	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13062461	0.80[ASN][1000 genomes]
rs13073901	0.85[EUR][1000 genomes]
rs13074289	0.85[EUR][1000 genomes]
rs13075686	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13077386	0.90[CEU][hapmap]
rs13078633	0.80[CHB][hapmap]
rs1355627	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1398340	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1398341	0.86[ASN][1000 genomes]
rs1398342	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1398344	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1398355	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1398356	0.87[EUR][1000 genomes]
rs1398357	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1398358	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1512511	0.86[ASN][1000 genomes]
rs1512512	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1512532	0.85[EUR][1000 genomes]
rs1512537	0.81[EUR][1000 genomes]
rs1877461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1913092	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1913093	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1913094	0.86[ASN][1000 genomes]
rs1913095	0.86[ASN][1000 genomes]
rs1913096	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1913097	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2089941	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2089942	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2175607	0.87[EUR][1000 genomes]
rs2175608	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2399329	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2399331	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2399332	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2399333	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3899903	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682009	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682010	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682011	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682013	0.86[ASN][1000 genomes]
rs4682186	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682187	0.87[EUR][1000 genomes]
rs61188814	0.88[EUR][1000 genomes]
rs6768646	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6768745	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6781525	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6781864	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7621339	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7628651	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9866331	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9874430	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999414	chr3:110103126-110340180	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv829670	chr3:110134650-110308256	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001144	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536687	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1001810	chr3:110158316-110522247	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv829672	chr3:110206693-110361632	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv460820	chr3:110283716-110321035	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv591274	chr3:110283716-110321035	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1007612	chr3:110296571-110310664	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1007973	chr3:110296571-110313934	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110293400-110301600	Weak transcription	Dnd41	blood
2	chr3:110296800-110301600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:110297000-110302600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:110297400-110301800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:110297400-110302200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:110298800-110308400	Weak transcription	K562	blood
7	chr3:110299000-110301800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:110299000-110302000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:110299000-110302200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:110299200-110301800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:110299400-110301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:110299400-110301800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:110299400-110302000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:110299400-110302200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:110299400-110302200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:110299400-110302200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:110299400-110302200	Weak transcription	HSMM	muscle
18	chr3:110299400-110302600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:110299400-110308000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:110299600-110302200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:110299600-110302200	Weak transcription	NH-A	brain
22	chr3:110299800-110301800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:110299800-110302200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:110299800-110307600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:110300400-110301200	ZNF genes & repeats	A549	lung
26	chr3:110300400-110302200	Weak transcription	Osteobl	bone
27	chr3:110300600-110301800	Weak transcription	NHDF-Ad	bronchial
28	chr3:110300800-110301200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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