Variant report

Variant	rs4336042
Chromosome Location	chr22:30552511-30552512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1468176	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548389	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807711	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs193471	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs193474	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193475	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193476	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2007446	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs2007458	0.89[CEU][hapmap]
rs2412972	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412976	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41165	0.89[CEU][hapmap]
rs41168	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs41171	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs41173	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs41176	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4820827	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823076	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753008	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753025	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753037	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763751	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763775	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763790	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5763842	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287570	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73164755	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap]
rs9306468	0.96[CEU][hapmap]
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	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
2	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
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4336042	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30541000-30555200	Weak transcription	Osteobl	bone
2	chr22:30547200-30555400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr22:30547200-30555600	Weak transcription	Thymus	Thymus
4	chr22:30550200-30555800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr22:30551600-30555600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:30552000-30553200	Enhancers	Fetal Intestine Small	intestine
7	chr22:30552200-30552800	Enhancers	Fetal Intestine Large	intestine
8	chr22:30552200-30554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr22:30552400-30553200	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links