Variant report

Variant	rs1548870
Chromosome Location	chr2:39868546-39868547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10177801	1.00[EUR][1000 genomes]
rs10208929	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124689	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12613210	0.98[EUR][1000 genomes]
rs12712652	0.88[EUR][1000 genomes]
rs12989245	0.88[EUR][1000 genomes]
rs13384364	0.83[EUR][1000 genomes]
rs13405084	0.84[EUR][1000 genomes]
rs13409487	0.88[EUR][1000 genomes]
rs1548871	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1861244	0.88[EUR][1000 genomes]
rs2041736	0.87[EUR][1000 genomes]
rs2058618	0.89[EUR][1000 genomes]
rs2215956	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2540200	0.90[EUR][1000 genomes]
rs2540215	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2540247	0.81[EUR][1000 genomes]
rs2540248	0.84[EUR][1000 genomes]
rs2540249	0.84[EUR][1000 genomes]
rs2540250	0.82[EUR][1000 genomes]
rs2540251	0.84[EUR][1000 genomes]
rs2540252	0.85[EUR][1000 genomes]
rs2540255	0.86[EUR][1000 genomes]
rs2716682	0.81[EUR][1000 genomes]
rs2716683	0.81[EUR][1000 genomes]
rs2716684	0.81[EUR][1000 genomes]
rs2716686	0.86[EUR][1000 genomes]
rs2716687	0.85[EUR][1000 genomes]
rs2716688	0.86[EUR][1000 genomes]
rs2716690	0.87[EUR][1000 genomes]
rs2716691	0.87[EUR][1000 genomes]
rs2716692	0.87[EUR][1000 genomes]
rs2716693	0.87[EUR][1000 genomes]
rs2716694	0.81[EUR][1000 genomes]
rs2716718	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2716719	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716720	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2716732	0.88[EUR][1000 genomes]
rs2716737	0.89[EUR][1000 genomes]
rs2716738	0.90[EUR][1000 genomes]
rs35791480	0.97[EUR][1000 genomes]
rs4670952	0.85[EUR][1000 genomes]
rs6736442	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748628	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917964	0.86[EUR][1000 genomes]
rs9309041	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs949812	0.88[EUR][1000 genomes]
rs949813	0.86[EUR][1000 genomes]
rs9679346	0.86[AMR][1000 genomes];0.84[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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39860000-39869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:39860400-39868800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:39860400-39869200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:39860600-39869000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:39861000-39869200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:39863400-39874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39864000-39868600	Weak transcription	Adipose Nuclei	Adipose
8	chr2:39866200-39868600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:39867200-39869200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:39867200-39870200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:39867200-39870200	Enhancers	NHLF	lung
12	chr2:39867400-39869000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:39867400-39869200	Weak transcription	Left Ventricle	heart
14	chr2:39867400-39869200	Enhancers	HSMM	muscle
15	chr2:39867400-39869400	Enhancers	Brain Hippocampus Middle	brain
16	chr2:39867400-39869400	Enhancers	HSMMtube	muscle
17	chr2:39867400-39870000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:39867600-39869000	Weak transcription	Brain Angular Gyrus	brain
19	chr2:39867600-39869200	Weak transcription	Right Atrium	heart
20	chr2:39867600-39869200	Weak transcription	Right Ventricle	heart
21	chr2:39867600-39875600	Weak transcription	Psoas Muscle	Psoas
22	chr2:39867800-39868800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:39867800-39868800	Weak transcription	Fetal Heart	heart
24	chr2:39867800-39869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:39868000-39870000	Enhancers	NHDF-Ad	bronchial
26	chr2:39868200-39868600	Weak transcription	HMEC	breast
27	chr2:39868200-39869000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:39868200-39869200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:39868200-39869200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:39868200-39869400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:39868200-39870200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:39868400-39869200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links