Variant report

Variant	rs10775449
Chromosome Location	chr18:29268845-29268846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10048377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11081706	0.85[YRI][hapmap]
rs11081707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11081708	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11660271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11664177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12327203	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12605321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964693	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551006	0.86[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs1614197	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17661533	1.00[YRI][hapmap]
rs1979105	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs34530749	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4799589	0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs718780	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8098191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968325	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10775449	DSC1	cis	parietal	SCAN
rs10775449	CDH2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29266400-29269200	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr18:29266400-29269400	Enhancers	Dnd41	blood
3	chr18:29267200-29269200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:29267200-29282600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr18:29267600-29269400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr18:29267600-29270200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr18:29268000-29269600	Enhancers	Primary hematopoietic stem cells	blood
8	chr18:29268000-29274000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:29268400-29269400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr18:29268600-29269000	Enhancers	Stomach Mucosa	stomach
11	chr18:29268600-29269400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:29268600-29269400	Enhancers	Fetal Thymus	thymus
13	chr18:29268600-29269400	Enhancers	Thymus	Thymus
14	chr18:29268800-29269600	Weak transcription	Adipose Nuclei	Adipose

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

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