Variant report

Variant	rs12345455
Chromosome Location	chr9:110032498-110032499
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110030231..110032782-chr9:110035060..110038842,3	MCF-7	breast:
2	chr9:110021549..110024530-chr9:110031690..110034147,2	MCF-7	breast:
3	chr9:110030757..110033354-chr9:110044206..110047003,3	MCF-7	breast:
4	chr9:110031224..110033017-chr9:110046490..110048325,2	K562	blood:
5	chr9:110007873..110010290-chr9:110031092..110033178,2	K562	blood:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10113916	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10119641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10122970	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481632	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10521083	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs10732368	0.84[CHB][hapmap]
rs10739232	0.87[CHB][hapmap]
rs10739234	0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs10739236	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739238	0.84[CHB][hapmap]
rs10759219	0.89[CHB][hapmap]
rs10759222	0.84[CHB][hapmap]
rs10816477	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs10816480	0.99[ASN][1000 genomes]
rs10816485	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10816490	0.87[ASN][1000 genomes]
rs10816491	0.87[ASN][1000 genomes]
rs10978767	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs10978769	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10978770	0.89[CHB][hapmap]
rs10978775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10978776	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978777	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978791	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12342066	1.00[ASN][1000 genomes]
rs12555417	1.00[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1535765	0.84[CHB][hapmap]
rs1535766	0.89[CHB][hapmap]
rs1805329	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1805332	0.84[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap]
rs1805334	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs1886134	0.84[CHB][hapmap]
rs2005143	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2147072	0.84[CHB][hapmap]
rs2417776	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417784	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2417785	0.84[CHB][hapmap]
rs28534368	0.89[ASN][1000 genomes]
rs28769087	0.98[ASN][1000 genomes]
rs28848858	1.00[ASN][1000 genomes]
rs4278207	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs4481670	0.83[CHB][hapmap]
rs4978849	0.83[CHB][hapmap]
rs61701375	0.92[ASN][1000 genomes]
rs67197321	0.88[AFR][1000 genomes]
rs698475	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7029997	0.84[CHB][hapmap]
rs7030169	0.84[CHB][hapmap]
rs7031906	0.84[CHB][hapmap]
rs7035611	0.84[CHB][hapmap];0.82[CHD][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs7036284	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap]
rs7040217	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041137	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs7046950	0.84[CHB][hapmap]
rs7852295	0.89[CHB][hapmap]
rs7866312	0.89[CHB][hapmap]
rs7866353	0.89[CHB][hapmap]
rs7866797	0.89[CHB][hapmap]
rs7867544	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs7873745	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs817836	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs817838	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817839	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817840	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817841	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817843	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817844	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817845	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817847	0.81[ASN][1000 genomes]
rs942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942293	0.84[CHB][hapmap]
rs9632893	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs9969728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12345455	KLF4	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110028200-110032800	Weak transcription	Pancreas	Pancrea
2	chr9:110029400-110032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:110029400-110035800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:110031400-110033400	Enhancers	Adipose Nuclei	Adipose
5	chr9:110031600-110032600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:110031600-110033000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr9:110031600-110033000	Enhancers	Fetal Intestine Small	intestine
8	chr9:110031600-110033200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:110031600-110033200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:110031600-110033200	Enhancers	Fetal Intestine Large	intestine
11	chr9:110031600-110033200	Enhancers	Placenta	Placenta
12	chr9:110031600-110033200	Enhancers	Ovary	ovary
13	chr9:110031600-110033200	Enhancers	HSMMtube	muscle
14	chr9:110031600-110033200	Enhancers	NHLF	lung
15	chr9:110031600-110033200	Enhancers	Osteobl	bone
16	chr9:110031600-110033400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:110031600-110033400	Enhancers	HMEC	breast
18	chr9:110031600-110033400	Enhancers	NHDF-Ad	bronchial
19	chr9:110031800-110032600	Enhancers	Liver	Liver
20	chr9:110031800-110032600	Weak transcription	HSMM	muscle
21	chr9:110031800-110033000	Flanking Active TSS	A549	lung
22	chr9:110031800-110033000	Flanking Active TSS	HepG2	liver
23	chr9:110031800-110033200	Enhancers	Fetal Lung	lung
24	chr9:110031800-110033200	Enhancers	Hela-S3	cervix
25	chr9:110032000-110033400	Enhancers	Stomach Mucosa	stomach
26	chr9:110032200-110032600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:110032200-110033000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:110032200-110033000	Enhancers	Duodenum Mucosa	Duodenum
29	chr9:110032200-110033200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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