Variant report

Variant	rs4024129
Chromosome Location	chr3:60064388-60064389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs212010	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2361336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2366953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2630182	1.00[JPT][hapmap]
rs2630205	1.00[JPT][hapmap]
rs2736763	1.00[JPT][hapmap]
rs34267930	0.90[ASN][1000 genomes]
rs4679629	1.00[JPT][hapmap]
rs4679631	1.00[JPT][hapmap]
rs4679636	1.00[JPT][hapmap]
rs6446109	1.00[JPT][hapmap]
rs6446110	1.00[JPT][hapmap]
rs67136973	0.90[ASN][1000 genomes]
rs6773600	1.00[JPT][hapmap]
rs6782148	1.00[JPT][hapmap]
rs6789112	1.00[JPT][hapmap]
rs6791450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6794055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6794069	0.81[ASN][1000 genomes]
rs6797474	1.00[JPT][hapmap]
rs6804216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6806074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7609578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7642268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9311748	0.90[ASN][1000 genomes]
rs969562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs986651	1.00[JPT][hapmap]

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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4024129	MARCKS	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60059800-60064800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:60061800-60066400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:60061800-60068400	Flanking Active TSS	Dnd41	blood
4	chr3:60062400-60064600	Weak transcription	Thymus	Thymus
5	chr3:60062400-60065200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:60062400-60066200	Weak transcription	Stomach Mucosa	stomach
7	chr3:60062400-60066400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:60062400-60066400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:60062800-60064800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:60063000-60066000	Weak transcription	Primary B cells from cord blood	blood
11	chr3:60063400-60066600	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr3:60063600-60065000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:60063600-60066000	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:60063600-60066800	Active TSS	Primary T cells fromperipheralblood	blood
15	chr3:60063800-60066400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr3:60063800-60068000	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:60064000-60064400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr3:60064000-60064400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:60064200-60064400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:60064200-60064600	Active TSS	Fetal Thymus	thymus
21	chr3:60064200-60066200	Active TSS	Primary T killer memory cells from peripheral blood	blood

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