Variant report

Variant	rs12911585
Chromosome Location	chr15:42934545-42934546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10162939	0.89[CEU][hapmap]
rs1058846	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638835	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1197550	0.89[CEU][hapmap]
rs1197551	0.89[CEU][hapmap]
rs12594855	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12902830	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903762	0.80[EUR][1000 genomes]
rs12905385	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs12908349	1.00[ASN][1000 genomes]
rs12914570	0.89[CEU][hapmap]
rs12915116	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs16957020	0.88[CEU][hapmap]
rs1705356	0.89[CEU][hapmap]
rs17774047	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136899	0.89[CEU][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs2175370	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3099758	0.89[CEU][hapmap]
rs34070722	0.89[EUR][1000 genomes]
rs34603230	0.87[EUR][1000 genomes]
rs34745458	1.00[ASN][1000 genomes]
rs35088691	1.00[ASN][1000 genomes]
rs35202249	1.00[ASN][1000 genomes]
rs35298309	1.00[ASN][1000 genomes]
rs35392023	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35538776	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs35738819	0.81[EUR][1000 genomes]
rs36092914	1.00[ASN][1000 genomes]
rs3742993	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs4545789	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4923950	0.82[EUR][1000 genomes]
rs4924690	0.89[CEU][hapmap]
rs4924691	0.89[CEU][hapmap]
rs4924692	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4924694	0.88[CEU][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs57298545	0.86[EUR][1000 genomes]
rs58938096	0.80[EUR][1000 genomes]
rs61122145	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623271	0.89[CEU][hapmap]
rs6493059	0.89[CEU][hapmap]
rs6493060	0.89[CEU][hapmap]
rs6493061	0.84[CEU][hapmap]
rs66932813	1.00[ASN][1000 genomes]
rs672054	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs71474496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7163030	0.84[CEU][hapmap]
rs7166373	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7169202	0.84[CEU][hapmap]
rs7176860	0.81[EUR][1000 genomes]
rs7183487	0.80[EUR][1000 genomes]
rs72713784	1.00[ASN][1000 genomes]
rs72713795	1.00[ASN][1000 genomes]
rs8023524	0.84[CEU][hapmap]
rs8024902	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8030587	0.94[CEU][hapmap]
rs8031218	0.94[CEU][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs8037613	1.00[ASN][1000 genomes]
rs8039711	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8039765	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes]
rs8043472	0.89[CEU][hapmap]
rs938047	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9920163	0.89[CEU][hapmap]
rs9944248	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12911585	CDAN1	cis	parietal	SCAN
rs12911585	BUB1B	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42898000-42967800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
3	chr15:42909600-42966400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:42915200-42940000	Weak transcription	HepG2	liver
5	chr15:42923000-42958200	Weak transcription	Hela-S3	cervix
6	chr15:42924400-42944600	Weak transcription	Thymus	Thymus
7	chr15:42925000-42936000	Strong transcription	Fetal Stomach	stomach
8	chr15:42925200-42966000	Weak transcription	NH-A	brain
9	chr15:42925200-42966800	Weak transcription	NHLF	lung
10	chr15:42925600-42961000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:42925800-42939200	Weak transcription	GM12878-XiMat	blood
12	chr15:42926400-42947200	Weak transcription	Fetal Brain Male	brain
13	chr15:42926800-42939400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:42928000-42935000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:42928200-42973600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:42928200-42974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:42928600-42934800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:42928600-42938600	Weak transcription	Small Intestine	intestine
19	chr15:42929600-42939600	Weak transcription	Liver	Liver
20	chr15:42929600-42942200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:42930000-42937400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:42930600-42964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:42930800-42957400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:42931000-42942400	Weak transcription	HMEC	breast
25	chr15:42931200-42938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:42931200-42949800	Weak transcription	Fetal Heart	heart
27	chr15:42931200-42954600	Weak transcription	Placenta	Placenta
28	chr15:42931200-42963400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:42931400-42934600	Weak transcription	HSMMtube	muscle
30	chr15:42931400-42938600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:42931400-42942400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:42931400-42944600	Weak transcription	NHDF-Ad	bronchial
33	chr15:42931400-42955800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:42931600-42938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:42931600-42942400	Weak transcription	Brain Substantia Nigra	brain
36	chr15:42931600-42942600	Weak transcription	Spleen	Spleen
37	chr15:42931600-42944000	Weak transcription	Left Ventricle	heart
38	chr15:42931600-42948800	Weak transcription	Brain Anterior Caudate	brain
39	chr15:42931600-42953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:42931600-42955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:42931800-42938600	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:42931800-42942200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:42931800-42955000	Weak transcription	Fetal Lung	lung
44	chr15:42931800-42955000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:42931800-42955600	Weak transcription	Lung	lung
46	chr15:42931800-42957200	Weak transcription	Primary B cells from cord blood	blood
47	chr15:42931800-42958200	Weak transcription	Brain Angular Gyrus	brain
48	chr15:42931800-42968000	Weak transcription	HSMM	muscle
49	chr15:42932000-42944600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:42932000-42944600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links