Variant report

Variant	rs10012406
Chromosome Location	chr4:120296884-120296885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10003953	1.00[AMR][1000 genomes]
rs10006040	0.85[AFR][1000 genomes]
rs10010097	1.00[AMR][1000 genomes]
rs10015714	1.00[AMR][1000 genomes]
rs10015999	1.00[AMR][1000 genomes]
rs10021318	1.00[AMR][1000 genomes]
rs10023384	1.00[AMR][1000 genomes]
rs10027735	1.00[AMR][1000 genomes]
rs10028634	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10029882	1.00[AMR][1000 genomes]
rs10031328	1.00[AMR][1000 genomes]
rs10032392	1.00[AMR][1000 genomes]
rs10213498	1.00[AMR][1000 genomes]
rs10471013	1.00[AMR][1000 genomes]
rs11098518	0.93[AFR][1000 genomes]
rs11098519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11098520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28380652	1.00[AMR][1000 genomes]
rs28399227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28405434	1.00[AMR][1000 genomes]
rs28436005	1.00[AMR][1000 genomes]
rs28450144	1.00[AMR][1000 genomes]
rs28461667	1.00[AMR][1000 genomes]
rs28469881	1.00[AMR][1000 genomes]
rs28510336	0.85[AFR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	1.00[AMR][1000 genomes]
rs28590285	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615474	1.00[AMR][1000 genomes]
rs28619175	1.00[AFR][1000 genomes]
rs28622207	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634062	1.00[AMR][1000 genomes]
rs28639494	1.00[AMR][1000 genomes]
rs28639769	1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	1.00[AMR][1000 genomes]
rs28864814	1.00[AMR][1000 genomes]
rs28870820	1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56191916	1.00[AMR][1000 genomes]
rs57295141	1.00[AMR][1000 genomes]
rs57469640	1.00[AFR][1000 genomes]
rs57516186	1.00[AMR][1000 genomes]
rs58691470	1.00[AFR][1000 genomes]
rs59116083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61729464	1.00[AMR][1000 genomes]
rs61823285	1.00[AMR][1000 genomes]
rs72914446	0.85[AFR][1000 genomes]
rs72914498	0.85[AFR][1000 genomes]
rs72918555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918590	1.00[AMR][1000 genomes]
rs72918597	1.00[AMR][1000 genomes]
rs72920607	1.00[AMR][1000 genomes]
rs72920619	1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9307478	1.00[AMR][1000 genomes]
rs9884290	1.00[AMR][1000 genomes]
rs9884542	1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	1.00[AMR][1000 genomes]
rs9997423	1.00[AMR][1000 genomes]
rs9998244	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120294600-120297000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr4:120295400-120297000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:120295400-120297800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr4:120295800-120297000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr4:120296000-120297000	Enhancers	Primary T cells from cord blood	blood
6	chr4:120296000-120297800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr4:120296800-120297000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:120296800-120297000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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