Variant report

Variant	rs2252288
Chromosome Location	chr1:179786005-179786006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179783903..179786438-chr1:179821262..179823436,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1014394	0.89[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1148820	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148821	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1299684	0.96[CEU][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2236589	0.81[CEU][hapmap]
rs2252384	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252388	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777912	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777914	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777915	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2794579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv520418	chr1:179761601-179794602	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv519307	chr1:179766086-179795505	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252288	TDRD5	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179783600-179786600	Enhancers	Lung	lung
2	chr1:179783600-179787000	Enhancers	Spleen	Spleen
3	chr1:179784600-179786200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:179784600-179786600	Weak transcription	HSMMtube	muscle
5	chr1:179784800-179786400	Weak transcription	HSMM	muscle
6	chr1:179784800-179787000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:179784800-179787000	Enhancers	Right Ventricle	heart
8	chr1:179784800-179787200	Enhancers	Right Atrium	heart
9	chr1:179784800-179788000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:179784800-179788200	Enhancers	NHLF	lung
11	chr1:179784800-179788400	Enhancers	Left Ventricle	heart
12	chr1:179785000-179786400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr1:179785000-179786400	Weak transcription	NHDF-Ad	bronchial
14	chr1:179785000-179786600	Weak transcription	Ovary	ovary
15	chr1:179785000-179788000	Enhancers	Adipose Nuclei	Adipose
16	chr1:179785000-179788000	Enhancers	Fetal Muscle Trunk	muscle
17	chr1:179785000-179788400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:179785000-179788600	Enhancers	Fetal Muscle Leg	muscle
19	chr1:179785000-179788800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:179785000-179788800	Weak transcription	Gastric	stomach
21	chr1:179785200-179786200	Enhancers	HUVEC	blood vessel
22	chr1:179785200-179787800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:179785200-179788200	Enhancers	Fetal Lung	lung
24	chr1:179785400-179786400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:179785400-179787000	Weak transcription	Colonic Mucosa	Colon
26	chr1:179785400-179787600	Weak transcription	Fetal Kidney	kidney
27	chr1:179785400-179788200	Weak transcription	NH-A	brain
28	chr1:179785600-179787600	Bivalent Enhancer	Placenta	Placenta
29	chr1:179785600-179787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:179785600-179788000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:179785800-179786600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:179786000-179787200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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