Variant report

Variant	rs12694841
Chromosome Location	chr2:231000108-231000109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:230994161..230996459-chr2:230999501..231001005,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10199897	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10209232	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10498243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933326	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11676757	0.83[EUR][1000 genomes]
rs11894286	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694838	0.84[AFR][1000 genomes]
rs12694840	0.82[AFR][1000 genomes]
rs13004807	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13420805	0.84[AFR][1000 genomes]
rs1365773	0.85[ASN][1000 genomes]
rs1365774	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1365775	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1427291	0.85[ASN][1000 genomes]
rs1529377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549567	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1549568	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1549569	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1549570	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1549571	0.85[ASN][1000 genomes]
rs2396712	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2396714	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2894694	0.83[ASN][1000 genomes]
rs4361119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436909	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436910	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6436912	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6706782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721137	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6735404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754313	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754451	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807953	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv875942	chr2:230959532-231008980	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875943	chr2:230960946-231027162	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12694841	SP110	cis	cerebellum	SCAN
rs12694841	ALPI	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:230994400-231000200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:230994600-231000200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:230996400-231002600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:230998800-231001400	Weak transcription	Spleen	Spleen
5	chr2:230999200-231000200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr2:230999200-231000200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:230999200-231000600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:230999200-231001200	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:230999200-231001400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:230999200-231001800	Weak transcription	NH-A	brain
11	chr2:230999400-231000200	Enhancers	Hela-S3	cervix
12	chr2:230999400-231000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:230999600-231000200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:230999600-231000400	Enhancers	Primary B cells from cord blood	blood
15	chr2:230999600-231000400	Enhancers	NHDF-Ad	bronchial
16	chr2:230999600-231002400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:230999800-231000400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:230999800-231000800	Enhancers	Adipose Nuclei	Adipose
19	chr2:230999800-231001000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:231000000-231000200	Enhancers	HUVEC	blood vessel
21	chr2:231000000-231000400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:231000000-231000400	Enhancers	Left Ventricle	heart
23	chr2:231000000-231000400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:231000000-231000600	Enhancers	GM12878-XiMat	blood
25	chr2:231000000-231002200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links