Variant report

Variant	rs6539262
Chromosome Location	chr12:106684765-106684766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106640373..106642748-chr12:106682387..106685392,3	MCF-7	breast:
2	chr12:106638556..106642995-chr12:106679966..106686733,8	MCF-7	breast:
3	chr12:106682888..106685086-chr12:106695950..106698366,2	MCF-7	breast:
4	chr12:106680059..106682241-chr12:106684339..106687312,2	K562	blood:
5	chr12:106679605..106682241-chr12:106684127..106685839,2	K562	blood:
6	chr12:106647187..106649805-chr12:106683824..106686258,2	MCF-7	breast:
7	chr12:106620350..106621264-chr12:106684714..106685651,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166046	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000258355	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10778462	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.98[ASN][1000 genomes]
rs10778463	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861573	0.97[ASN][1000 genomes]
rs11831752	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1392176	0.98[ASN][1000 genomes]
rs1532586	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243506	0.81[GIH][hapmap];1.00[LWK][hapmap]
rs2250262	1.00[LWK][hapmap]
rs2250441	1.00[LWK][hapmap];0.84[MKK][hapmap]
rs2252685	0.81[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs2253838	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs4964460	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs6539263	0.98[ASN][1000 genomes]
rs6539264	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs7296927	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7297359	0.97[ASN][1000 genomes]
rs7298576	0.91[ASN][1000 genomes]
rs7957421	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7965175	1.00[ASN][1000 genomes]
rs7965616	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794382	chr12:106679812-106699151	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539262	NUAK1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106678600-106688800	Weak transcription	Lung	lung
2	chr12:106680000-106695200	Weak transcription	Right Atrium	heart
3	chr12:106682800-106685200	Weak transcription	Fetal Intestine Small	intestine
4	chr12:106683000-106685000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:106683000-106685400	Weak transcription	Fetal Intestine Large	intestine
6	chr12:106683200-106693000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:106683400-106685400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:106683400-106689600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106683400-106689800	Weak transcription	Hela-S3	cervix
10	chr12:106683600-106689800	Weak transcription	NHEK	skin
11	chr12:106683800-106689600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:106684400-106685600	Enhancers	Stomach Mucosa	stomach
13	chr12:106684400-106691400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:106684600-106684800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr12:106684600-106685400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:106684600-106685600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:106684600-106685600	Enhancers	A549	lung
18	chr12:106684600-106685800	Enhancers	HepG2	liver

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