Variant report

Variant	rs10981859
Chromosome Location	chr9:116413354-116413355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116224389..116227414-chr9:116412116..116415236,3	MCF-7	breast:
2	chr9:116356338..116358088-chr9:116413316..116415073,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS3-2	chr9:116413236-116413444	ENSG00000227482

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10817497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981860	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4978551	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4979270	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	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
4	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116407000-116413600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:116410200-116413400	Enhancers	Fetal Heart	heart
3	chr9:116410200-116413400	Enhancers	NHDF-Ad	bronchial
4	chr9:116410400-116413600	Enhancers	Fetal Muscle Leg	muscle
5	chr9:116410400-116413800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:116410400-116415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:116410600-116413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:116410600-116413400	Enhancers	NHLF	lung
9	chr9:116410600-116413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:116410800-116414800	Weak transcription	Fetal Intestine Large	intestine
11	chr9:116411000-116413600	Enhancers	Fetal Stomach	stomach
12	chr9:116411000-116415000	Weak transcription	Fetal Intestine Small	intestine
13	chr9:116411000-116416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:116411200-116413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:116411200-116413400	Enhancers	Ovary	ovary
16	chr9:116411200-116415400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:116411400-116413800	Enhancers	HUVEC	blood vessel
18	chr9:116411400-116415400	Enhancers	Osteobl	bone
19	chr9:116411400-116416600	Weak transcription	Adipose Nuclei	Adipose
20	chr9:116411600-116413400	Enhancers	NH-A	brain
21	chr9:116411600-116420000	Weak transcription	Fetal Brain Female	brain
22	chr9:116411800-116417800	Enhancers	Liver	Liver
23	chr9:116412000-116414000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116412000-116414200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:116412000-116414200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:116412000-116414200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:116412000-116414800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:116412000-116415000	Weak transcription	Right Atrium	heart
29	chr9:116412000-116415000	Weak transcription	Right Ventricle	heart
30	chr9:116412000-116416400	Weak transcription	Fetal Lung	lung
31	chr9:116412200-116415400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr9:116412200-116417200	Weak transcription	Brain Anterior Caudate	brain
33	chr9:116412200-116417400	Weak transcription	Brain Angular Gyrus	brain
34	chr9:116412200-116417400	Weak transcription	Brain Substantia Nigra	brain
35	chr9:116412200-116417600	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:116412400-116413400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:116412400-116413400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:116412400-116413400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr9:116412400-116413400	Flanking Active TSS	HepG2	liver
40	chr9:116412400-116414000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:116412400-116417200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:116412600-116413400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr9:116412600-116413400	Enhancers	Fetal Kidney	kidney
44	chr9:116412600-116413400	Flanking Active TSS	A549	lung
45	chr9:116412600-116413600	Enhancers	H9 Cell Line	embryonic stem cell
46	chr9:116412600-116413600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
47	chr9:116412600-116413800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:116412600-116414000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr9:116412600-116414200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr9:116412600-116417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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