Variant report

Variant	rs28536201
Chromosome Location	chr9:98276753-98276754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf102-10	chr9:98276327-98276802	ENSG00000271659.1

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10512248	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355619	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355620	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909919	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066829	0.83[ASN][1000 genomes]
rs2236407	0.83[ASN][1000 genomes]
rs2282042	0.84[ASN][1000 genomes]
rs2297086	0.83[ASN][1000 genomes]
rs2297088	0.83[ASN][1000 genomes]
rs28457763	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495472	0.83[ASN][1000 genomes]
rs28496034	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28504650	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28557305	0.84[ASN][1000 genomes]
rs28591501	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28620668	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758302	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448343	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS 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	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98273800-98277800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:98274000-98277800	Weak transcription	Gastric	stomach
3	chr9:98274200-98277400	Active TSS	Rectal Smooth Muscle	rectum
4	chr9:98274200-98278000	Weak transcription	Aorta	Aorta
5	chr9:98274400-98277200	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr9:98274400-98277600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:98274400-98277600	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:98274400-98278000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:98274600-98278000	Weak transcription	Pancreas	Pancrea
10	chr9:98274600-98279600	Active TSS	Duodenum Mucosa	Duodenum
11	chr9:98274800-98277800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98274800-98278200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:98275000-98277400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:98275000-98277600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:98275000-98277600	Weak transcription	Brain Angular Gyrus	brain
16	chr9:98275000-98277600	Weak transcription	Brain Anterior Caudate	brain
17	chr9:98275000-98277600	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:98275000-98277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:98275000-98277600	Weak transcription	Esophagus	oesophagus
20	chr9:98275000-98277800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:98275000-98277800	Weak transcription	Left Ventricle	heart
22	chr9:98275000-98277800	Weak transcription	HMEC	breast
23	chr9:98275000-98277800	Weak transcription	HSMM	muscle
24	chr9:98275200-98276800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:98275200-98277400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:98275200-98277400	Weak transcription	Colonic Mucosa	Colon
27	chr9:98275200-98277600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:98275200-98277600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:98275200-98277600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:98275200-98277600	Weak transcription	Ovary	ovary
31	chr9:98275200-98277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98275200-98277800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:98275200-98277800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr9:98275200-98278000	Weak transcription	Lung	lung
35	chr9:98275200-98278000	Weak transcription	Right Atrium	heart
36	chr9:98275200-98278000	Weak transcription	HSMMtube	muscle
37	chr9:98275400-98276800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:98275400-98277600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:98275400-98277600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:98275400-98277600	Weak transcription	NHLF	lung
41	chr9:98275400-98277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:98275400-98277800	Weak transcription	Right Ventricle	heart
43	chr9:98275400-98277800	Weak transcription	NHEK	skin
44	chr9:98275400-98278000	Weak transcription	Spleen	Spleen
45	chr9:98275600-98277600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:98275600-98278600	Weak transcription	Hela-S3	cervix
47	chr9:98275800-98276800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr9:98275800-98277000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:98275800-98277200	Active TSS	Fetal Intestine Large	intestine
50	chr9:98275800-98277400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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