Variant report

Variant	rs12039667
Chromosome Location	chr1:46790764-46790765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10789488	0.86[AMR][1000 genomes]
rs10890386	0.81[AMR][1000 genomes]
rs10890387	0.83[AMR][1000 genomes]
rs10890388	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890389	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584233	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11586229	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11590411	0.81[ASN][1000 genomes]
rs12125573	0.81[AMR][1000 genomes]
rs1547180	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2093044	0.94[ASN][1000 genomes]
rs4660343	0.81[AMR][1000 genomes]
rs4660918	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4660919	0.82[AMR][1000 genomes]
rs4660920	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4660921	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6429596	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7527133	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv947254	chr1:46769363-46808918	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 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	chr1:46773400-46805400	Weak transcription	Right Atrium	heart
2	chr1:46777400-46799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46781800-46805400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:46783400-46791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:46783400-46799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:46783600-46790800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:46783600-46790800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:46783600-46791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:46783600-46797400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:46784000-46799400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:46784000-46805000	Weak transcription	Thymus	Thymus
12	chr1:46786000-46796800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:46787000-46793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:46787200-46794600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:46787400-46793800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:46789400-46790800	Enhancers	GM12878-XiMat	blood

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