Variant report

Variant	rs10989088
Chromosome Location	chr9:98823407-98823408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98636264..98639064-chr9:98822222..98824808,3	MCF-7	breast:
2	chr9:98814315..98817027-chr9:98823230..98826158,2	MCF-7	breast:
3	chr9:98254155..98254770-chr9:98823287..98824045,2	MCF-7	breast:
4	chr9:98819421..98821017-chr9:98821751..98824395,2	MCF-7	breast:
5	chr9:98822681..98824476-chr9:98825586..98827527,2	K562	blood:
6	chr22:46512027..46512895-chr9:98823217..98823802,2	K562	blood:
7	chr9:98823291..98823799-chr9:98980239..98980879,2	MCF-7	breast:
8	chr18:26822794..26823359-chr9:98823022..98823769,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10819780	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547203	1.00[ASN][1000 genomes]
rs1547204	1.00[ASN][1000 genomes]
rs4592147	1.00[ASN][1000 genomes]
rs7029255	0.99[ASN][1000 genomes]
rs7048174	0.97[ASN][1000 genomes]
rs734631	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927968	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv1809137	chr9:98798752-98823646	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv982606	chr9:98814728-98823757	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10989088	ERCC6L2	cis	Artery Tibial	GTEx
rs10989088	C9orf102	cis	multi-tissue	Pritchard
rs10989088	LOC57653	cis	parietal	SCAN
rs10989088	IPPK	cis	cerebellum	SCAN
rs10989088	C9orf130	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98810200-98827200	Weak transcription	Aorta	Aorta
2	chr9:98812200-98829600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:98812800-98829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:98815200-98824600	Weak transcription	Fetal Brain Male	brain
5	chr9:98816000-98823800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:98819800-98823800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:98819800-98832000	Weak transcription	Gastric	stomach
8	chr9:98823000-98823800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:98823000-98824200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:98823000-98824800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr9:98823200-98823800	Enhancers	A549	lung
12	chr9:98823200-98824000	Enhancers	Adipose Nuclei	Adipose
13	chr9:98823200-98824000	Enhancers	NHEK	skin
14	chr9:98823200-98824200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:98823200-98824200	Enhancers	Brain Cingulate Gyrus	brain
16	chr9:98823200-98824200	Enhancers	Brain Hippocampus Middle	brain
17	chr9:98823200-98824200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr9:98823200-98824200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:98823200-98824200	Enhancers	Brain Substantia Nigra	brain
20	chr9:98823200-98824400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:98823200-98824400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:98823200-98824400	Enhancers	Placenta	Placenta
23	chr9:98823200-98824400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:98823200-98824400	Enhancers	Stomach Mucosa	stomach
25	chr9:98823200-98824600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:98823200-98824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:98823200-98824600	Enhancers	Fetal Muscle Leg	muscle
28	chr9:98823200-98824800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:98823200-98824800	Enhancers	Duodenum Mucosa	Duodenum
30	chr9:98823200-98825000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:98823200-98825200	Enhancers	Spleen	Spleen
32	chr9:98823200-98825800	Enhancers	Fetal Stomach	stomach
33	chr9:98823200-98827600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:98823400-98823600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:98823400-98823600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:98823400-98823600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
37	chr9:98823400-98823600	Enhancers	Fetal Kidney	kidney
38	chr9:98823400-98823600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr9:98823400-98823600	Bivalent Enhancer	NH-A	brain
40	chr9:98823400-98824000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:98823400-98824000	Enhancers	Stomach Smooth Muscle	stomach
42	chr9:98823400-98824200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr9:98823400-98824200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:98823400-98824200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr9:98823400-98824200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:98823400-98824200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:98823400-98824200	Enhancers	Brain Angular Gyrus	brain
48	chr9:98823400-98824200	Enhancers	Brain Anterior Caudate	brain
49	chr9:98823400-98824200	Enhancers	Esophagus	oesophagus
50	chr9:98823400-98824200	Enhancers	Pancreas	Pancrea

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