Variant report

Variant	rs62490366
Chromosome Location	chr7:150374741-150374742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIMAP6-2	chr7:150374599-150374748	NONHSAT124146

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12154435	0.96[ASN][1000 genomes]
rs12154436	0.96[ASN][1000 genomes]
rs12154687	0.85[ASN][1000 genomes]
rs1234356	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1234357	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234361	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12397707	0.84[ASN][1000 genomes]
rs12532045	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535208	0.85[ASN][1000 genomes]
rs12703091	0.86[ASN][1000 genomes]
rs1316352	0.96[ASN][1000 genomes]
rs13220967	0.85[ASN][1000 genomes]
rs13225905	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226190	0.90[ASN][1000 genomes]
rs13230583	0.86[ASN][1000 genomes]
rs13234724	0.89[ASN][1000 genomes]
rs13238412	0.86[ASN][1000 genomes]
rs13240099	0.85[ASN][1000 genomes]
rs13240106	0.85[ASN][1000 genomes]
rs1403220	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542143	0.90[ASN][1000 genomes]
rs34030180	0.95[ASN][1000 genomes]
rs34396063	0.96[ASN][1000 genomes]
rs34585329	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34940374	0.92[ASN][1000 genomes]
rs35283918	0.91[ASN][1000 genomes]
rs35285840	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329030	0.96[ASN][1000 genomes]
rs35342751	0.86[ASN][1000 genomes]
rs35760614	0.91[ASN][1000 genomes]
rs36020504	0.96[ASN][1000 genomes]
rs36065681	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735086	0.86[ASN][1000 genomes]
rs56138121	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279394	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56325059	0.86[ASN][1000 genomes]
rs56412316	0.96[ASN][1000 genomes]
rs59468128	0.95[ASN][1000 genomes]
rs62490361	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491810	0.86[ASN][1000 genomes]
rs62491812	0.90[ASN][1000 genomes]
rs62491814	0.92[ASN][1000 genomes]
rs62491829	0.96[ASN][1000 genomes]
rs73474862	0.96[ASN][1000 genomes]
rs954395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62490366	GIMAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150370000-150377000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr7:150371800-150377200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr7:150372000-150375200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:150372000-150375600	Enhancers	Primary hematopoietic stem cells	blood
5	chr7:150372000-150376200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:150372000-150376400	Enhancers	Fetal Thymus	thymus
7	chr7:150373200-150375000	Weak transcription	Adipose Nuclei	Adipose
8	chr7:150373200-150376000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:150373200-150380800	Weak transcription	Thymus	Thymus
10	chr7:150373400-150375000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:150373800-150375800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:150373800-150376000	Enhancers	Dnd41	blood
13	chr7:150373800-150377200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:150374000-150375200	Enhancers	HUVEC	blood vessel
15	chr7:150374000-150375600	Enhancers	Primary T cells from cord blood	blood
16	chr7:150374000-150375600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr7:150374000-150376800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr7:150374000-150377000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:150374000-150380400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:150374200-150375600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:150374200-150376200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:150374200-150380400	Weak transcription	GM12878-XiMat	blood
23	chr7:150374400-150376600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr7:150374600-150375400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr7:150374600-150375800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links