Variant report

Variant	rs2675089
Chromosome Location	chr2:183914247-183914248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17265880	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6734848	0.85[EUR][1000 genomes]
rs6739840	0.85[EUR][1000 genomes]
rs72886535	0.85[EUR][1000 genomes]
rs72886536	0.85[EUR][1000 genomes]
rs72886597	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888442	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888444	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888445	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888453	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888459	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72888467	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72888485	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72888487	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7575613	0.83[EUR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675089	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183904400-183921600	Weak transcription	K562	blood
2	chr2:183913200-183915800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:183913400-183917800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:183914200-183914400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:183914200-183914400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:183914200-183914400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:183914200-183914600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:183914200-183914600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:183914200-183914800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:183914200-183915000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:183914200-183915000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:183914200-183915000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:183914200-183916600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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

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