Variant report

Variant	rs891722
Chromosome Location	chr9:116929476-116929477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF12-3	chr9:116929050-116929727	NONHSAT134369

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1431821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1560538	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1864724	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2043196	0.95[ASN][1000 genomes]
rs2567706	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2567707	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2567722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2567724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2808770	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808771	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808774	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808775	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2808776	0.86[CHB][hapmap]
rs2808778	0.88[CHB][hapmap]
rs2808779	0.86[CHB][hapmap]
rs2808780	0.86[CHB][hapmap]
rs2808784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2808785	0.85[CHB][hapmap]
rs2808790	0.94[ASN][1000 genomes]
rs2808795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2808796	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2808797	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2808798	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4481685	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4588934	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57113194	0.83[ASN][1000 genomes]
rs730619	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs891727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893752	chr9:116899258-116944333	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466527	chr9:116907448-116933449	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv615228	chr9:116907448-116933449	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv466529	chr9:116907553-116930194	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv615229	chr9:116907553-116930194	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv466530	chr9:116916931-116935660	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv615230	chr9:116916931-116935660	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv466531	chr9:116916931-116940418	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv615231	chr9:116916931-116940418	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv3357134	chr9:116925431-116930729	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919000-116936600	Weak transcription	Brain Hippocampus Middle	brain
2	chr9:116919000-116937600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:116919400-116930000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
6	chr9:116921800-116931600	Weak transcription	Aorta	Aorta
7	chr9:116925800-116931800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:116926000-116929800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:116926000-116929800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:116926000-116930000	Weak transcription	Esophagus	oesophagus
11	chr9:116926000-116931600	Weak transcription	Spleen	Spleen
12	chr9:116926000-116937200	Weak transcription	Gastric	stomach
13	chr9:116926200-116930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:116926200-116930000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:116926200-116930400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:116926200-116934800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:116926200-116937400	Weak transcription	Right Ventricle	heart
18	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:116926400-116931000	Weak transcription	NH-A	brain
20	chr9:116926400-116931600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:116926400-116932000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:116926400-116934400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:116926400-116935200	Weak transcription	Left Ventricle	heart
24	chr9:116926400-116935400	Weak transcription	Right Atrium	heart
25	chr9:116926400-116937000	Weak transcription	Stomach Mucosa	stomach
26	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:116926600-116930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:116926600-116930400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:116926600-116932400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:116926600-116939400	Weak transcription	Fetal Kidney	kidney
32	chr9:116926800-116929800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:116926800-116929800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:116926800-116929800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:116926800-116930000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:116926800-116930200	Weak transcription	Lung	lung
37	chr9:116926800-116930200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:116926800-116930400	Weak transcription	A549	lung
39	chr9:116926800-116930600	Weak transcription	Fetal Thymus	thymus
40	chr9:116926800-116934600	Weak transcription	HMEC	breast
41	chr9:116926800-116937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:116927000-116929800	Weak transcription	Pancreas	Pancrea
43	chr9:116927000-116931400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:116927000-116932400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:116927000-116933400	Strong transcription	HepG2	liver
46	chr9:116927200-116930000	Weak transcription	Adipose Nuclei	Adipose
47	chr9:116928200-116932400	Strong transcription	Fetal Intestine Large	intestine
48	chr9:116928400-116929600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:116928400-116929600	Enhancers	Osteobl	bone
50	chr9:116928400-116929800	Weak transcription	Liver	Liver

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