Variant report

Variant	rs2411293
Chromosome Location	chr15:39766553-39766554
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:39766178-39767425	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000259269	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11070204	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1158918	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633970	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857561	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438465	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593294	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12899217	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812583	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947782	0.89[ASN][1000 genomes]
rs1993892	0.89[ASN][1000 genomes]
rs1993893	0.86[ASN][1000 genomes]
rs2086166	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2127029	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34329697	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244571	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4486853	0.92[EUR][1000 genomes]
rs4924361	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924363	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59431794	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60697424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7171244	0.93[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7180041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7350779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74008200	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74010438	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030260	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8033214	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9888722	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9920539	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39759800-39766800	Weak transcription	Lung	lung
2	chr15:39759800-39770800	Weak transcription	Stomach Mucosa	stomach
3	chr15:39762600-39767200	Enhancers	Colon Smooth Muscle	Colon
4	chr15:39762800-39767200	Enhancers	Fetal Stomach	stomach
5	chr15:39763000-39767800	Enhancers	Fetal Lung	lung
6	chr15:39763200-39767800	Enhancers	Fetal Muscle Leg	muscle
7	chr15:39763400-39767000	Enhancers	Rectal Smooth Muscle	rectum
8	chr15:39763400-39767200	Enhancers	NHDF-Ad	bronchial
9	chr15:39763800-39766600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:39764000-39767000	Enhancers	NHLF	lung
11	chr15:39764400-39767000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:39764600-39767000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:39764600-39767000	Enhancers	Adipose Nuclei	Adipose
14	chr15:39764600-39767000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:39764600-39767200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:39764800-39767200	Enhancers	HSMMtube	muscle
17	chr15:39765200-39767200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:39765200-39767200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr15:39765200-39767800	Enhancers	Pancreas	Pancrea
20	chr15:39765200-39767800	Enhancers	HSMM	muscle
21	chr15:39765600-39766600	Weak transcription	NH-A	brain
22	chr15:39765600-39767800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:39765600-39767800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:39765800-39766800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:39765800-39766800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:39765800-39767000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:39766000-39766600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr15:39766000-39767000	Enhancers	Stomach Smooth Muscle	stomach
29	chr15:39766000-39768000	Enhancers	Fetal Kidney	kidney
30	chr15:39766200-39766800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr15:39766200-39767000	Enhancers	Placenta	Placenta
32	chr15:39766200-39767200	Weak transcription	Fetal Intestine Large	intestine
33	chr15:39766200-39767800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:39766200-39767800	Enhancers	HUVEC	blood vessel
35	chr15:39766400-39767000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr15:39766400-39767000	Enhancers	Spleen	Spleen
37	chr15:39766400-39767200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr15:39766400-39767200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links