Variant report

Variant	rs1006444
Chromosome Location	chr2:133787580-133787581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1025697	1.00[CHB][hapmap]
rs10928440	1.00[CHB][hapmap]
rs12467278	1.00[CHB][hapmap]
rs12470656	1.00[CHB][hapmap]
rs12473775	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000201	1.00[CHB][hapmap]
rs13033108	1.00[CHB][hapmap]
rs1347709	1.00[CHB][hapmap]
rs1368969	1.00[CHB][hapmap]
rs1370600	0.80[GIH][hapmap]
rs1434223	1.00[CHB][hapmap]
rs1434229	1.00[CHB][hapmap]
rs1437901	1.00[ASN][1000 genomes]
rs1437902	0.86[ASN][1000 genomes]
rs1437909	1.00[JPT][hapmap]
rs17733147	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17735890	1.00[CHB][hapmap]
rs17736771	1.00[CHB][hapmap]
rs17792341	1.00[CHB][hapmap]
rs17792473	1.00[CHB][hapmap]
rs17798750	1.00[CHB][hapmap]
rs1821426	1.00[CHB][hapmap]
rs1821427	1.00[CHB][hapmap]
rs1836222	1.00[CHB][hapmap]
rs2320541	1.00[ASN][1000 genomes]
rs59818946	1.00[ASN][1000 genomes]
rs61133672	0.86[ASN][1000 genomes]
rs6720246	1.00[CHB][hapmap]
rs6756592	1.00[CHB][hapmap]
rs7558369	1.00[CHB][hapmap]
rs7561032	1.00[CHB][hapmap]
rs7588373	1.00[CHB][hapmap]
rs7598823	1.00[CHB][hapmap]
rs7603712	1.00[CHB][hapmap]
rs893411	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956343	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834382	chr2:133728399-133891418	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999703	chr2:133734955-133817962	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535926	chr2:133734955-133817962	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv875139	chr2:133777866-133929225	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006444	NCKAP5	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133762600-133797200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:133784600-133787600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:133784600-133789200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:133784800-133789000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:133784800-133789000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links