Variant report

Variant	rs2997683
Chromosome Location	chr9:72707396-72707397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-1	chr9:72707167-72707622	ENSG00000204706.10

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1180089	0.84[GIH][hapmap]
rs12000536	1.00[EUR][1000 genomes]
rs12003723	1.00[EUR][1000 genomes]
rs12004033	1.00[EUR][1000 genomes]
rs12004037	1.00[EUR][1000 genomes]
rs12005031	1.00[EUR][1000 genomes]
rs17086970	1.00[EUR][1000 genomes]
rs17088359	1.00[EUR][1000 genomes]
rs1927110	0.85[AFR][1000 genomes]
rs1927111	1.00[EUR][1000 genomes]
rs2309645	0.84[GIH][hapmap]
rs2975869	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975870	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975871	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975872	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975873	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975874	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975875	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975876	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975878	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975881	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975882	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975883	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975884	0.85[AFR][1000 genomes]
rs2975885	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975886	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2975887	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997667	1.00[EUR][1000 genomes]
rs2997688	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997689	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997691	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997692	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997694	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997695	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997697	0.82[AFR][1000 genomes]
rs2997698	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997699	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997700	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997701	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997702	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997703	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997704	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997705	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2997706	0.93[AFR][1000 genomes]
rs3015190	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015191	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015193	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015194	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015195	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015196	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015197	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015198	0.85[AFR][1000 genomes]
rs3015199	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015201	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015202	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015203	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015205	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015206	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015208	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015209	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015210	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015212	0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015214	0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015215	1.00[GIH][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3015222	1.00[EUR][1000 genomes]
rs58773163	1.00[EUR][1000 genomes]
rs60836347	1.00[EUR][1000 genomes]
rs73449454	1.00[EUR][1000 genomes]
rs73449465	1.00[EUR][1000 genomes]
rs73458494	1.00[EUR][1000 genomes]
rs73460527	1.00[EUR][1000 genomes]
rs73460530	1.00[EUR][1000 genomes]
rs73650530	1.00[EUR][1000 genomes]
rs7862220	1.00[EUR][1000 genomes]
rs943535	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72694800-72708200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr9:72694800-72721400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:72695400-72709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:72696400-72708800	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:72698200-72708800	Weak transcription	Psoas Muscle	Psoas
6	chr9:72698800-72711200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:72699000-72708800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:72703200-72711600	Enhancers	Colon Smooth Muscle	Colon
9	chr9:72704800-72708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:72705400-72709400	Enhancers	Rectal Smooth Muscle	rectum
11	chr9:72705600-72707800	Enhancers	Stomach Smooth Muscle	stomach
12	chr9:72705800-72707600	Enhancers	HSMMtube	muscle
13	chr9:72706000-72710200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:72706200-72709000	Weak transcription	HSMM	muscle
15	chr9:72706200-72710000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:72706400-72708400	Weak transcription	Ovary	ovary
17	chr9:72706400-72708800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:72706600-72707400	Enhancers	Brain Germinal Matrix	brain
19	chr9:72706600-72707400	Enhancers	Fetal Brain Female	brain
20	chr9:72706800-72708200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:72706800-72708600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:72706800-72709200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:72707000-72707600	Enhancers	Left Ventricle	heart
24	chr9:72707000-72708200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:72707200-72707400	Enhancers	Pancreas	Pancrea
26	chr9:72707200-72707400	Enhancers	Right Ventricle	heart
27	chr9:72707200-72709000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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