Variant report

Variant	rs1927106
Chromosome Location	chr9:72728699-72728700
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-2	chr9:72728671-72728782	ENSG00000237778.1
2	lnc-KLF9-1	chr9:72728671-72728782	NONHSAT131793
3	lnc-KLF9-1	chr9:72728671-72728782	NONHSAT131797
4	lnc-KLF9-1	chr9:72728671-72728776	ENSG00000204706.10
5	lnc-KLF9-1	chr9:72728671-72728776	ENSG00000204706.10

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1007127	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10481740	1.00[ASN][1000 genomes]
rs10481741	1.00[ASN][1000 genomes]
rs10735583	1.00[ASN][1000 genomes]
rs10780811	1.00[ASN][1000 genomes]
rs10868799	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11142350	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1536956	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1927115	0.94[ASN][1000 genomes]
rs1927128	0.81[ASN][1000 genomes]
rs1927139	0.81[ASN][1000 genomes]
rs2026136	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2148861	0.94[ASN][1000 genomes]
rs2182739	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2209779	0.99[ASN][1000 genomes]
rs2281935	0.89[ASN][1000 genomes]
rs2309633	0.81[ASN][1000 genomes]
rs2975862	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2975890	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975907	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2975908	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2975910	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2975915	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2975917	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2997652	0.85[ASN][1000 genomes]
rs2997664	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2997676	0.93[ASN][1000 genomes]
rs2997677	0.93[ASN][1000 genomes]
rs2997678	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3015168	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3015224	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015232	0.89[ASN][1000 genomes]
rs3015238	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015242	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4375070	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4744968	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4744977	1.00[ASN][1000 genomes]
rs4744978	1.00[ASN][1000 genomes]
rs6560019	0.81[ASN][1000 genomes]
rs7027209	0.94[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv949052	chr9:72698039-72741247	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72714800-72742400	Weak transcription	Aorta	Aorta
2	chr9:72722000-72729600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:72722000-72758400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:72724200-72729200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:72724400-72742600	Weak transcription	Right Ventricle	heart
6	chr9:72725000-72728800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:72725000-72728800	Genic enhancers	Stomach Smooth Muscle	stomach
8	chr9:72725200-72728800	Enhancers	HMEC	breast
9	chr9:72725200-72735800	Weak transcription	Fetal Brain Male	brain
10	chr9:72725600-72728800	Enhancers	Stomach Mucosa	stomach
11	chr9:72725600-72735400	Weak transcription	Right Atrium	heart
12	chr9:72725600-72740400	Weak transcription	Fetal Lung	lung
13	chr9:72725600-72745200	Weak transcription	Lung	lung
14	chr9:72725800-72728800	Enhancers	HepG2	liver
15	chr9:72725800-72742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:72725800-72764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:72726000-72729200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:72726000-72729200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:72726000-72729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:72726000-72729600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:72726000-72731400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:72726000-72734600	Weak transcription	Adipose Nuclei	Adipose
23	chr9:72726000-72735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:72726200-72741000	Weak transcription	Fetal Stomach	stomach
25	chr9:72726200-72749200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:72726600-72728800	Enhancers	NHEK	skin
27	chr9:72726600-72730000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:72726800-72728800	Strong transcription	Fetal Muscle Leg	muscle
29	chr9:72726800-72729600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:72726800-72730000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:72726800-72731000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:72726800-72734800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:72727000-72729800	Strong transcription	Ovary	ovary
35	chr9:72727000-72740400	Weak transcription	Esophagus	oesophagus
36	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:72727200-72735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:72727200-72737800	Weak transcription	Pancreas	Pancrea
39	chr9:72727200-72746600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:72727600-72728800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:72727800-72728800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:72728000-72728800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:72728000-72730000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr9:72728200-72729000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:72728200-72729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:72728200-72729800	Strong transcription	HSMM	muscle
47	chr9:72728200-72730200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:72728200-72732800	Strong transcription	HSMMtube	muscle
49	chr9:72728200-72752800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:72728200-72758400	Weak transcription	Rectal Mucosa Donor 29	rectum

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