Variant report

Variant	rs12029988
Chromosome Location	chr1:221948869-221948870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10495177	0.89[ASN][1000 genomes]
rs10863658	0.83[ASN][1000 genomes]
rs11588738	0.90[ASN][1000 genomes]
rs12040332	0.82[ASN][1000 genomes]
rs12565255	0.81[ASN][1000 genomes]
rs12568507	0.82[ASN][1000 genomes]
rs12726313	0.98[ASN][1000 genomes]
rs35907150	0.85[ASN][1000 genomes]
rs4240927	0.80[ASN][1000 genomes]
rs4240929	0.83[ASN][1000 genomes]
rs4297303	0.93[ASN][1000 genomes]
rs4846723	0.85[ASN][1000 genomes]
rs4846724	0.86[ASN][1000 genomes]
rs4846726	0.85[ASN][1000 genomes]
rs7523844	0.96[ASN][1000 genomes]
rs7526577	0.96[ASN][1000 genomes]
rs9441956	0.80[ASN][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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12029988	USH2A	cis	parietal	SCAN
rs12029988		cis	Lymphoblastoid	GTEx
rs12029988	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221945400-221949600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:221947400-221949600	Weak transcription	Hela-S3	cervix
3	chr1:221947600-221952000	Weak transcription	Spleen	Spleen
4	chr1:221947600-221953600	Weak transcription	Lung	lung
5	chr1:221948200-221950000	Weak transcription	Stomach Mucosa	stomach
6	chr1:221948200-221950000	Weak transcription	HUVEC	blood vessel
7	chr1:221948600-221950600	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:221948600-221951000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:221948600-221951200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:221948800-221949000	Enhancers	Adipose Nuclei	Adipose
11	chr1:221948800-221951400	Enhancers	Primary B cells from cord blood	blood
12	chr1:221948800-221955000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:221948800-221958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links