Variant report

Variant	rs5763775
Chromosome Location	chr22:30503007-30503008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30502959..30506188-chr22:30648757..30654246,8	MCF-7	breast:
2	chr22:30502809..30506298-chr22:30639806..30643736,4	MCF-7	breast:
3	chr22:30502612..30504825-chr22:30819472..30821124,2	MCF-7	breast:
4	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128342	Chromatin interaction
ENSG00000268812	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1468176	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548389	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1807711	0.83[EUR][1000 genomes]
rs193471	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs193474	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193475	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193476	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2007446	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2007458	0.89[CEU][hapmap]
rs2285667	0.87[AMR][1000 genomes]
rs2412972	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412976	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41156	0.81[AFR][1000 genomes]
rs41157	0.81[AFR][1000 genomes]
rs41161	0.87[AMR][1000 genomes]
rs41165	0.89[CEU][hapmap]
rs41168	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs41170	0.84[AFR][1000 genomes]
rs41171	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs41173	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41176	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4336042	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820827	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4823076	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753008	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5753025	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753037	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763614	0.80[AMR][1000 genomes]
rs5763670	0.87[AMR][1000 genomes]
rs5763751	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763790	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763842	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59663694	0.85[AMR][1000 genomes]
rs6006315	0.82[YRI][hapmap]
rs7287570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73162764	0.85[AMR][1000 genomes]
rs73164755	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap]
rs9306468	0.96[CEU][hapmap]
rs960987	0.80[AMR][1000 genomes]
rs997913	0.89[CEU][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763775	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30501200-30504400	Weak transcription	NH-A	brain
2	chr22:30501400-30505800	Enhancers	A549	lung
3	chr22:30501600-30503200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr22:30501600-30504400	Weak transcription	HSMM	muscle
5	chr22:30501800-30511800	Weak transcription	Osteobl	bone
6	chr22:30502000-30503600	Enhancers	Dnd41	blood
7	chr22:30502000-30504600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr22:30502600-30504400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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