Variant report

Variant	rs10179549
Chromosome Location	chr2:77524377-77524378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10170684	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126601	0.80[CEU][hapmap]
rs11904768	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12614215	0.80[CEU][hapmap]
rs13422362	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1441047	0.93[CHB][hapmap]
rs17013938	0.80[CEU][hapmap]
rs17013942	0.80[CEU][hapmap]
rs290039	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs290042	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs290043	0.94[ASN][1000 genomes]
rs290046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs401204	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs475859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4853310	0.80[CEU][hapmap]
rs693782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7602394	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs920517	0.91[JPT][hapmap]
rs920518	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv874333	chr2:77315349-77798886	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv518504	chr2:77326832-78172786	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1004938	chr2:77347740-78186543	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv535783	chr2:77347740-78186543	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv529904	chr2:77347741-78186542	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv997329	chr2:77354560-78176285	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv874336	chr2:77515995-77568716	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10179549	ALMS1P	cis	cerebellum	SCAN
rs10179549	C2orf7	cis	cerebellum	SCAN
rs10179549	ACTG2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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