Variant report

Variant	rs3958027
Chromosome Location	chr22:30244835-30244836
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs131293	0.81[AMR][1000 genomes]
rs131295	0.84[AMR][1000 genomes]
rs140145	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs140147	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs140149	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs140150	0.80[AMR][1000 genomes]
rs17711377	0.84[AMR][1000 genomes]
rs2007446	0.96[CEU][hapmap]
rs2007458	0.89[CEU][hapmap]
rs2057882	0.80[AMR][1000 genomes]
rs2074706	0.84[AMR][1000 genomes]
rs2074707	0.84[AMR][1000 genomes]
rs2079338	0.84[AMR][1000 genomes]
rs2301402	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28749829	0.86[AMR][1000 genomes]
rs41165	0.89[CEU][hapmap]
rs41168	0.96[CEU][hapmap]
rs41171	0.96[CEU][hapmap]
rs41173	0.96[CEU][hapmap]
rs5752964	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs5752973	0.81[EUR][1000 genomes]
rs5752975	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs5752978	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763559	0.81[EUR][1000 genomes]
rs5763565	0.80[EUR][1000 genomes]
rs5763614	0.82[EUR][1000 genomes]
rs5997529	0.81[AMR][1000 genomes]
rs5997530	0.80[AMR][1000 genomes]
rs5997535	0.81[AMR][1000 genomes]
rs5997546	0.81[EUR][1000 genomes]
rs5997549	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6006274	0.87[AMR][1000 genomes]
rs6006288	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs713656	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs7287434	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737911	0.92[CEU][hapmap];0.86[AFR][1000 genomes]
rs740041	0.84[AMR][1000 genomes]
rs9306465	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs9306468	0.96[CEU][hapmap];0.86[AFR][1000 genomes]
rs960987	0.81[EUR][1000 genomes]
rs9614077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614102	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs997913	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3958027	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30243400-30245600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr22:30243600-30245000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr22:30243600-30245000	Enhancers	Adipose Nuclei	Adipose
4	chr22:30244000-30245000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr22:30244200-30245800	Enhancers	Fetal Muscle Leg	muscle
6	chr22:30244400-30245000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr22:30244400-30245000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr22:30244600-30245000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr22:30244800-30245000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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