Variant report

Variant	rs6006288
Chromosome Location	chr22:30265022-30265023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1076135	0.92[ASN][1000 genomes]
rs12710565	0.86[EUR][1000 genomes]
rs131293	0.81[AMR][1000 genomes]
rs131295	0.84[AMR][1000 genomes]
rs140145	0.86[AMR][1000 genomes]
rs140147	0.85[AMR][1000 genomes]
rs140149	0.86[AMR][1000 genomes]
rs17711377	0.84[AMR][1000 genomes]
rs1807513	0.87[EUR][1000 genomes]
rs1894474	0.92[ASN][1000 genomes]
rs2007446	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2074706	0.84[AMR][1000 genomes]
rs2074707	0.84[AMR][1000 genomes]
rs2079338	0.84[AMR][1000 genomes]
rs2189802	0.86[EUR][1000 genomes]
rs2285667	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301402	0.83[AMR][1000 genomes]
rs28749829	0.86[AMR][1000 genomes]
rs3958027	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41156	0.86[AFR][1000 genomes]
rs41157	0.86[AFR][1000 genomes]
rs41161	0.81[EUR][1000 genomes]
rs41170	0.86[AFR][1000 genomes]
rs4630869	0.88[EUR][1000 genomes]
rs55805200	0.88[EUR][1000 genomes]
rs5752964	0.84[AMR][1000 genomes]
rs5752973	0.90[EUR][1000 genomes]
rs5752975	0.89[EUR][1000 genomes]
rs5752978	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763559	0.90[EUR][1000 genomes]
rs5763565	0.89[EUR][1000 genomes]
rs5763581	0.85[EUR][1000 genomes]
rs5763589	0.86[EUR][1000 genomes]
rs5763591	0.87[EUR][1000 genomes]
rs5763592	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5763614	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763670	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59663694	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997529	0.81[AMR][1000 genomes]
rs5997535	0.81[AMR][1000 genomes]
rs5997546	0.90[EUR][1000 genomes]
rs5997549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006274	0.87[AMR][1000 genomes]
rs6006300	0.85[EUR][1000 genomes]
rs713656	0.84[AMR][1000 genomes]
rs7285583	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7287434	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7289604	0.81[EUR][1000 genomes]
rs73162764	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737939	0.85[EUR][1000 genomes]
rs740041	0.84[AMR][1000 genomes]
rs9306465	0.86[AMR][1000 genomes]
rs960987	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9614077	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9614100	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9614102	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1851082	chr22:30253256-30294744	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	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
rs6006288	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30258200-30267600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr22:30261200-30265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:30263800-30265800	Weak transcription	HMEC	breast
4	chr22:30263800-30265800	Weak transcription	NHEK	skin
5	chr22:30263800-30267600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr22:30264400-30265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:30264400-30266600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr22:30264400-30266800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr22:30264600-30266800	Weak transcription	Fetal Heart	heart
10	chr22:30265000-30267200	Weak transcription	Fetal Brain Male	brain

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