Variant report

Variant	rs3890027
Chromosome Location	chr13:48758205-48758206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11839064	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359861	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17071466	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1752134	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1854177	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406803	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2765076	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35537731	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500616	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942755	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942756	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942758	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs551034	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56762281	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637390	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637831	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7318104	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322824	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73485008	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7981621	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7982500	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984127	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987321	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7988173	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988389	0.81[ASN][1000 genomes]
rs7994451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7998964	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8000847	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526458	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526459	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534981	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534986	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534995	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs956169	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9591144	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9591146	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9595871	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3327569	chr13:48743550-48798094	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48749800-48760200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr13:48755200-48762800	Enhancers	Primary B cells from cord blood	blood
3	chr13:48755600-48760000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr13:48755600-48760000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr13:48755600-48760200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:48755800-48759600	Enhancers	Primary T cells from cord blood	blood
7	chr13:48755800-48760200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr13:48755800-48763000	Enhancers	Primary B cells from peripheral blood	blood
9	chr13:48756000-48760000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr13:48756200-48760400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:48756200-48760400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr13:48756400-48759200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:48756400-48759400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr13:48756600-48760000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr13:48756800-48760800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr13:48757000-48760200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr13:48757000-48760400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr13:48757200-48760000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr13:48757400-48763200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:48758000-48763000	Enhancers	Fetal Thymus	thymus
21	chr13:48758000-48763200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr13:48758000-48763400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:48758200-48759000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:48758200-48759200	Enhancers	GM12878-XiMat	blood
25	chr13:48758200-48760200	Enhancers	Dnd41	blood
26	chr13:48758200-48760400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:48758200-48762600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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