Variant report

Variant	rs28707603
Chromosome Location	chr4:122112254-122112255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10009822	1.00[AMR][1000 genomes]
rs10017221	1.00[AMR][1000 genomes]
rs10021787	0.83[AMR][1000 genomes]
rs11938699	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17051305	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17051318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28452005	0.83[AMR][1000 genomes]
rs28452943	1.00[AMR][1000 genomes]
rs28567402	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28572759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28600934	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28669888	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6534255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6534256	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6817294	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6825601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6840309	0.83[AMR][1000 genomes]
rs6845343	0.83[AMR][1000 genomes]
rs6847595	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847834	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6852366	0.83[AMR][1000 genomes]
rs7682759	0.83[AMR][1000 genomes]
rs7684215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684241	1.00[AMR][1000 genomes]
rs7684464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684586	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9784553	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9992473	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9992978	1.00[AMR][1000 genomes]
rs9995558	0.83[AMR][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	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879860	chr4:122030864-122126808	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122107800-122113400	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:122108800-122114000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:122109600-122113400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr4:122109600-122113800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:122111200-122113400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr4:122111200-122114000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:122111200-122114000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:122111200-122114400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:122111400-122113200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:122111400-122114400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:122111600-122113200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr4:122111600-122113800	Enhancers	Thymus	Thymus
13	chr4:122111800-122113400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr4:122111800-122113800	Enhancers	Dnd41	blood
15	chr4:122111800-122114000	Weak transcription	GM12878-XiMat	blood
16	chr4:122112000-122112400	Enhancers	Primary T cells from cord blood	blood
17	chr4:122112000-122112400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr4:122112200-122113200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:122112200-122113200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:122112200-122113200	Weak transcription	Fetal Thymus	thymus

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