Variant report

Variant	rs951466
Chromosome Location	chr6:132720623-132720624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1416100	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1577995	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061243	1.00[ASN][1000 genomes]
rs17190773	1.00[ASN][1000 genomes]
rs2153176	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34871318	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032364	1.00[ASN][1000 genomes]
rs3861470	1.00[ASN][1000 genomes]
rs55753187	1.00[ASN][1000 genomes]
rs55779505	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56067804	1.00[ASN][1000 genomes]
rs56172786	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336490	1.00[ASN][1000 genomes]
rs66578544	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925224	1.00[ASN][1000 genomes]
rs72994859	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994861	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994866	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994871	1.00[ASN][1000 genomes]
rs72994872	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994875	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739846	1.00[ASN][1000 genomes]
rs7755527	1.00[ASN][1000 genomes]
rs7755532	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773683	1.00[ASN][1000 genomes]
rs951467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830811	chr6:132623160-132787539	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv886675	chr6:132683762-132730947	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv604668	chr6:132687248-132731358	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs951466	SPATS2L	trans	lymphoblastoid	seeQTL
rs951466	VNN1	cis	lymphoblastoid	seeQTL
rs951466	MOXD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132714000-132721200	Weak transcription	NH-A	brain
2	chr6:132714400-132720800	Weak transcription	HSMMtube	muscle
3	chr6:132714800-132721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:132715200-132721800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:132718400-132721000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:132718400-132721400	Weak transcription	Esophagus	oesophagus
7	chr6:132718800-132721200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:132719200-132721400	Weak transcription	Fetal Stomach	stomach
9	chr6:132719400-132720800	Weak transcription	Fetal Brain Female	brain
10	chr6:132719800-132723200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:132720000-132722000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:132720000-132722800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:132720400-132720800	Enhancers	GM12878-XiMat	blood
14	chr6:132720400-132721400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:132720400-132721400	Active TSS	Fetal Kidney	kidney
16	chr6:132720400-132721800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:132720400-132723000	Active TSS	NHDF-Ad	bronchial
18	chr6:132720600-132720800	Enhancers	Fetal Lung	lung
19	chr6:132720600-132721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:132720600-132721400	Enhancers	NHEK	skin
21	chr6:132720600-132721600	Flanking Active TSS	Osteobl	bone
22	chr6:132720600-132723400	Active TSS	NHLF	lung
23	chr6:132720600-132723600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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