Variant report

Variant	rs11229030
Chromosome Location	chr11:57203009-57203010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11820985	0.82[CHB][hapmap]
rs11828218	0.82[CHB][hapmap];0.82[GIH][hapmap]
rs12422015	0.82[CHB][hapmap]
rs2264054	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581925	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2584859	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729389	0.82[CHB][hapmap]
rs4477456	0.82[CHB][hapmap]
rs4529894	0.82[CHB][hapmap]
rs7948027	0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.83[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	22412388	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11229030	OR4A15	cis	cerebellum	SCAN
rs11229030	OR5T2	cis	parietal	SCAN
rs11229030	DTX4	cis	cerebellum	SCAN
rs11229030	PATL1	cis	parietal	SCAN
rs11229030	SLC43A3	cis	cerebellum	SCAN
rs11229030	TIMM10	cis	cerebellum	SCAN
rs11229030	SLC43A1	cis	cerebellum	SCAN
rs11229030	ZP1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57199200-57203800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:57200000-57205600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:57200400-57208000	Weak transcription	Lung	lung
4	chr11:57202000-57210200	Enhancers	Liver	Liver
5	chr11:57202600-57203800	Enhancers	A549	lung
6	chr11:57202800-57203600	Weak transcription	K562	blood
7	chr11:57202800-57205600	Weak transcription	Esophagus	oesophagus
8	chr11:57203000-57205600	Weak transcription	Fetal Intestine Small	intestine
9	chr11:57203000-57205600	Weak transcription	HepG2	liver
10	chr11:57203000-57205800	Weak transcription	Fetal Intestine Large	intestine

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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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