Variant report

Variant	rs3759041
Chromosome Location	chr11:64827087-64827088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
NAALADL1	TF binding region
ENSG00000149792	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000146670	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12362669	0.81[EUR][1000 genomes]
rs12363102	0.81[EUR][1000 genomes]
rs1300845	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2458298	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs2507814	1.00[CEU][hapmap]
rs35661464	0.81[EUR][1000 genomes]
rs3741390	0.86[AMR][1000 genomes]
rs3850946	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3850947	0.83[CEU][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs4258384	0.81[EUR][1000 genomes]
rs476824	0.82[EUR][1000 genomes]
rs486984	0.96[CEU][hapmap]
rs488686	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs502333	0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs533018	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs562590	0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs566221	0.81[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs947799	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3759041	SNX15	cis	parietal	SCAN
rs3759041	RAB1B	cis	parietal	SCAN
rs3759041	LRRN4CL	cis	parietal	SCAN
rs3759041	B3GAT3	cis	cerebellum	SCAN
rs3759041	SPDYC	cis	parietal	SCAN
rs3759041	MARK2	cis	cerebellum	SCAN
rs3759041	SNX15	cis	Muscle Skeletal	GTEx
rs3759041	SCGB2A2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64813800-64833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:64814000-64827600	Weak transcription	Pancreas	Pancrea
3	chr11:64821400-64828800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:64822400-64829800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
6	chr11:64824600-64827200	Weak transcription	GM12878-XiMat	blood
7	chr11:64825400-64831000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:64825800-64828800	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr11:64826000-64827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:64826200-64827600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:64826400-64827200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:64826400-64827400	Weak transcription	Colonic Mucosa	Colon
13	chr11:64826400-64827400	Weak transcription	Fetal Intestine Large	intestine
14	chr11:64826400-64827400	Weak transcription	Fetal Intestine Small	intestine
15	chr11:64826400-64828400	Enhancers	Duodenum Mucosa	Duodenum
16	chr11:64826400-64828800	Enhancers	HepG2	liver
17	chr11:64827000-64827200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:64827000-64828000	Enhancers	Spleen	Spleen
19	chr11:64827000-64828200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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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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