Variant report

Variant	rs1411780
Chromosome Location	chr10:90578539-90578540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11202898	1.00[CHD][hapmap]
rs11202902	1.00[CHD][hapmap]
rs12254856	1.00[CHD][hapmap]
rs1653842	1.00[CHD][hapmap]
rs1769692	1.00[CHD][hapmap]
rs2439707	1.00[CHD][hapmap]
rs303525	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs303526	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs376036	1.00[CHD][hapmap]
rs378308	1.00[CHD][hapmap]
rs390436	1.00[CHD][hapmap]
rs3910679	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs407433	1.00[CHD][hapmap]
rs434401	1.00[CHD][hapmap]
rs442545	1.00[CHD][hapmap]
rs451949	1.00[CHD][hapmap]
rs454439	1.00[CHD][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1411780	ANKRD22	cis	Skin Sun Exposed Lower leg	GTEx
rs1411780	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90570600-90584200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr10:90573400-90583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:90574200-90598400	Weak transcription	Gastric	stomach
4	chr10:90575600-90580200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:90576000-90580000	Weak transcription	Small Intestine	intestine
6	chr10:90577200-90580200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr10:90577200-90580600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:90577400-90579400	Weak transcription	Primary T cells from cord blood	blood
9	chr10:90577600-90579200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:90577800-90580200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr10:90578000-90579200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:90578000-90580600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr10:90578000-90607200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:90578400-90582600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:90578400-90591600	Weak transcription	Fetal Stomach	stomach

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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

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