Variant report

Variant	rs9969728
Chromosome Location	chr9:110039634-110039635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110037191..110040266-chr9:110043063..110045811,4	K562	blood:
2	chr9:110034708..110043058-chr9:110043083..110050663,16	MCF-7	breast:
3	chr9:110038034..110040721-chr9:110051893..110053905,2	MCF-7	breast:
4	chr9:110037400..110041134-chr9:110041455..110046032,7	K562	blood:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10122970	0.90[AMR][1000 genomes];0.93[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];0.83[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];0.89[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];0.84[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	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978777	0.93[AMR][1000 genomes];0.97[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]
rs12345455	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]
rs12555417	1.00[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1535765	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
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	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2147071	0.80[EUR][1000 genomes]
rs2147072	0.84[CHB][hapmap]
rs2417776	0.90[AMR][1000 genomes];0.94[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]
rs4978844	0.81[EUR][1000 genomes]
rs4978849	0.83[CHB][hapmap]
rs61701375	0.92[ASN][1000 genomes]
rs67197321	0.84[AFR][1000 genomes]
rs698475	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7019341	0.81[EUR][1000 genomes]
rs7029997	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7030169	0.84[CHB][hapmap]
rs7030631	0.80[EUR][1000 genomes]
rs7031906	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7035611	0.84[CHB][hapmap];0.82[CHD][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7036284	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap];0.80[EUR][1000 genomes]
rs7039041	0.80[EUR][1000 genomes]
rs7040217	0.90[AMR][1000 genomes];0.97[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];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs7043962	0.80[EUR][1000 genomes]
rs7046950	0.84[CHB][hapmap]
rs7852295	0.89[CHB][hapmap]
rs7856227	0.80[EUR][1000 genomes]
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];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs7873745	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817839	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817840	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817841	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817843	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817844	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817845	0.89[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942293	0.84[CHB][hapmap]
rs9632893	0.94[CHB][hapmap];0.81[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
rs9969728	KLF4	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110035600-110040200	Enhancers	NHLF	lung
2	chr9:110035600-110040400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:110035600-110040400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:110035600-110044600	Enhancers	Placenta	Placenta
5	chr9:110035800-110040200	Enhancers	HSMMtube	muscle
6	chr9:110035800-110040400	Enhancers	Fetal Heart	heart
7	chr9:110036000-110039800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr9:110036000-110040000	Enhancers	Osteobl	bone
9	chr9:110036200-110040400	Enhancers	Fetal Muscle Leg	muscle
10	chr9:110036400-110044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:110037800-110040000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:110037800-110044000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:110038000-110039800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:110038000-110040000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:110038000-110042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:110038000-110042200	Weak transcription	NHEK	skin
17	chr9:110038000-110043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:110038000-110044400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:110038000-110044400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:110038000-110044400	Weak transcription	NH-A	brain
21	chr9:110038200-110040000	Enhancers	NHDF-Ad	bronchial
22	chr9:110038200-110042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:110038200-110042200	Weak transcription	HMEC	breast
24	chr9:110038400-110043200	Weak transcription	GM12878-XiMat	blood
25	chr9:110038600-110040400	Enhancers	Fetal Stomach	stomach
26	chr9:110039000-110040600	Weak transcription	Ovary	ovary
27	chr9:110039000-110042800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:110039000-110043000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:110039200-110040400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr9:110039400-110039800	Enhancers	Colon Smooth Muscle	Colon
31	chr9:110039400-110039800	Enhancers	A549	lung
32	chr9:110039400-110042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:110039600-110039800	Enhancers	Adipose Nuclei	Adipose
34	chr9:110039600-110040200	Genic enhancers	HSMM	muscle
35	chr9:110039600-110043400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:110039600-110044400	Weak transcription	Rectal Smooth Muscle	rectum

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