Variant report

Variant	rs1011179
Chromosome Location	chr11:19097299-19097300
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10833054	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1125217	0.83[EUR][1000 genomes]
rs12802650	0.90[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1503500	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7945401	0.82[EUR][1000 genomes]
rs905552	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9633837	1.00[YRI][hapmap]

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	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv897030	chr11:19049478-19106045	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1011179	SAA3P	cis	cerebellum	SCAN
rs1011179	SPTY2D1	cis	cerebellum	SCAN
rs1011179	NAV2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19093400-19098200	Weak transcription	HUVEC	blood vessel
2	chr11:19093400-19098800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:19093600-19098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:19095200-19101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:19095200-19101000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:19095200-19104000	Weak transcription	Esophagus	oesophagus
7	chr11:19095800-19098200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:19095800-19098800	Weak transcription	Adipose Nuclei	Adipose
9	chr11:19096200-19098200	Weak transcription	Gastric	stomach
10	chr11:19096200-19098400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:19096200-19101000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:19096200-19102200	Weak transcription	Pancreas	Pancrea
13	chr11:19096400-19098200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:19096400-19098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:19097000-19098000	Weak transcription	Stomach Mucosa	stomach
16	chr11:19097000-19100800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:19097000-19102400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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