Variant report

Variant	rs2106107
Chromosome Location	chr22:29835987-29835988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP1B1-1	chr22:29833006-29838118	ENSG00000225465.4
2	lnc-AP1B1-1	chr22:29832818-29838118	NONHSAT084700
3	lnc-AP1B1-1	chr22:29833004-29838118	NONHSAT084701
4	lnc-AP1B1-1	chr22:29833007-29838118	NONHSAT084702
5	lnc-AP1B1-1	chr22:29833007-29838118	NONHSAT084703
6	lnc-AP1B1-1	chr22:29833016-29838118	NONHSAT084704
7	lnc-AP1B1-1	chr22:29832818-29838118	ENSG00000225465.6

No data

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12484045	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484086	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484859	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12485237	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13053624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13053758	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13053817	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13054354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13054504	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13055259	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13055671	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13055707	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13056528	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13057382	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13057815	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13058617	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13340033	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987627	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2157714	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34305567	0.96[EUR][1000 genomes]
rs35040119	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56148436	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56305531	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56355388	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66659089	0.86[EUR][1000 genomes]
rs67613029	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67660453	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71324766	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71329484	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71329485	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71329486	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71329487	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71329488	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287166	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7290684	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7290855	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7292216	0.95[EUR][1000 genomes]
rs73405097	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1060197	chr22:29817507-29842511	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv964618	chr22:29833351-29836403	Weak transcription Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2106107	NIPSNAP1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29831400-29849800	Weak transcription	Fetal Intestine Small	intestine
2	chr22:29834200-29850200	Weak transcription	Ovary	ovary
3	chr22:29834600-29836600	Weak transcription	Brain Anterior Caudate	brain
4	chr22:29835400-29836000	Weak transcription	Fetal Brain Female	brain
5	chr22:29835600-29839000	Weak transcription	Brain Hippocampus Middle	brain
6	chr22:29835800-29836000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links