Variant report

Variant	rs13402331
Chromosome Location	chr2:57947440-57947441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10186791	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10195687	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10196378	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10204616	0.85[EUR][1000 genomes]
rs10496076	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13418015	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290867	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2678908	0.82[CEU][hapmap]
rs2717001	0.82[CEU][hapmap]
rs2717002	0.82[CEU][hapmap]
rs2717006	0.86[CEU][hapmap]
rs3886275	0.88[EUR][1000 genomes]
rs6720888	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57938400-57947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:57938400-57952400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:57939600-57947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:57939600-57947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:57939800-57948200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:57941800-57948200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:57943400-57948200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:57945400-57947800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:57945400-57947800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:57945400-57948200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:57947000-57948000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:57947200-57947600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:57947200-57948200	Enhancers	Fetal Thymus	thymus
14	chr2:57947400-57947600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:57947400-57948000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:57947400-57948000	Enhancers	HSMM	muscle

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links