Variant report

Variant	rs6487785
Chromosome Location	chr12:29361021-29361022
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10771487	0.95[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10771488	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10771490	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10843339	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12372303	0.91[EUR][1000 genomes]
rs12372311	0.91[EUR][1000 genomes]
rs12372469	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1496212	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1561131	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1865768	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1908689	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs3858548	0.91[EUR][1000 genomes]
rs4930855	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4931160	0.93[EUR][1000 genomes]
rs4931161	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6487779	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6487781	0.93[EUR][1000 genomes]
rs6487784	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136626	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7297280	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7961901	1.00[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs7962453	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7970668	0.99[EUR][1000 genomes]
rs7971179	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6487785	TSPAN11	cis	parietal	SCAN
rs6487785	IFLTD1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29325400-29364600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:29358000-29362400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:29358200-29361600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:29358400-29362000	Enhancers	Primary hematopoietic stem cells	blood
5	chr12:29359200-29364000	Enhancers	Fetal Intestine Small	intestine
6	chr12:29359200-29366400	Enhancers	Fetal Intestine Large	intestine
7	chr12:29359400-29361400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:29359600-29361400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr12:29360200-29362800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:29360400-29361800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr12:29360400-29363600	Weak transcription	Small Intestine	intestine
12	chr12:29360400-29381000	Weak transcription	HUVEC	blood vessel
13	chr12:29360600-29361200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:29360600-29362600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:29360800-29361400	Enhancers	Adipose Nuclei	Adipose
16	chr12:29360800-29361400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr12:29360800-29361800	Enhancers	Duodenum Mucosa	Duodenum
18	chr12:29361000-29361400	Enhancers	Fetal Kidney	kidney
19	chr12:29361000-29361800	Enhancers	Colonic Mucosa	Colon
20	chr12:29361000-29362600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:29361000-29364600	Enhancers	Sigmoid Colon	Sigmoid Colon

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