Variant report

Variant	rs2808779
Chromosome Location	chr9:116934501-116934502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116930014..116932339-chr9:116933734..116935674,2	MCF-7	breast:
2	chr9:116932183..116936074-chr9:116938591..116942808,3	K562	blood:
3	chr9:116933656..116936282-chr9:116947384..116950321,2	MCF-7	breast:
4	chr9:116930264..116933030-chr9:116933706..116935267,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF618-2	chr9:116933576-116935890	NONHSAT134370

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1431821	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs1545001	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1560538	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2567706	0.86[CHB][hapmap];0.95[CHD][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2567722	0.86[CHB][hapmap]
rs2567724	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2808770	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808771	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808774	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808775	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2808776	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808777	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808778	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2808780	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808784	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2808795	0.86[CHB][hapmap]
rs4481685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7855790	0.83[MEX][hapmap]
rs891722	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
8	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
9	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
10	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
11	nsv466532	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv615232	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
14	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2808779	ZNF483	cis	cerebellum	SCAN

Chromatin state (count:78 , 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	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
5	chr9:116926000-116937200	Weak transcription	Gastric	stomach
6	chr9:116926200-116934800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:116926200-116937400	Weak transcription	Right Ventricle	heart
8	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:116926400-116935200	Weak transcription	Left Ventricle	heart
10	chr9:116926400-116935400	Weak transcription	Right Atrium	heart
11	chr9:116926400-116937000	Weak transcription	Stomach Mucosa	stomach
12	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:116926600-116939400	Weak transcription	Fetal Kidney	kidney
15	chr9:116926800-116934600	Weak transcription	HMEC	breast
16	chr9:116926800-116937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:116928800-116935600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:116929000-116937000	Weak transcription	HSMM	muscle
19	chr9:116929200-116934600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:116929200-116937800	Weak transcription	HUVEC	blood vessel
21	chr9:116929400-116937200	Weak transcription	HSMMtube	muscle
22	chr9:116929800-116936000	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr9:116930000-116934800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:116930000-116938800	Genic enhancers	Fetal Muscle Leg	muscle
25	chr9:116930200-116934600	Weak transcription	Adipose Nuclei	Adipose
26	chr9:116930400-116936200	Strong transcription	A549	lung
27	chr9:116930400-116937200	Weak transcription	Lung	lung
28	chr9:116930600-116937000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:116930600-116937200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:116930800-116935400	Weak transcription	Esophagus	oesophagus
32	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
33	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:116931400-116934600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:116932000-116935200	Weak transcription	Aorta	Aorta
36	chr9:116932200-116938600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:116932600-116934800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:116932600-116935000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:116932600-116935200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:116932600-116935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:116932600-116936800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:116932600-116938000	Enhancers	Fetal Thymus	thymus
43	chr9:116932800-116934600	Weak transcription	NHDF-Ad	bronchial
44	chr9:116932800-116935800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:116932800-116939200	Weak transcription	Osteobl	bone
46	chr9:116932800-116943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:116933000-116934600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:116933000-116935600	Weak transcription	Colonic Mucosa	Colon
50	chr9:116933000-116939400	Weak transcription	Fetal Lung	lung

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