Variant report

Variant	rs10988521
Chromosome Location	chr9:101760905-101760906
allele	C/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101611820..101612398-chr9:101760720..101761431,2	K562	blood:
2	chr9:101757724..101761274-chr9:101835762..101837823,3	K562	blood:
3	chr9:101622815..101623852-chr9:101760749..101761771,5	MCF-7	breast:
4	chr9:101760174..101763909-chr9:101764160..101767138,3	K562	blood:
5	chr9:101610013..101612448-chr9:101759740..101762487,2	MCF-7	breast:
6	chr9:101622816..101623807-chr9:101760819..101761758,4	K562	blood:
7	chr9:101760174..101761965-chr9:101764160..101766601,2	K562	blood:
8	chr9:101736926..101737820-chr9:101760843..101761915,4	MCF-7	breast:
9	chr9:101568251..101569109-chr9:101760833..101761361,2	MCF-7	breast:
10	chr9:101610533..101611669-chr9:101760817..101761806,13	K562	blood:
11	chr9:101757461..101761274-chr9:101835859..101838201,6	K562	blood:
12	chr9:101571089..101573557-chr9:101759747..101761480,2	MCF-7	breast:
13	chr9:101736884..101738167-chr9:101760897..101761815,6	MCF-7	breast:
14	chr9:101755503..101758615-chr9:101759001..101763298,4	K562	blood:
15	chr9:101610463..101611441-chr9:101760900..101761817,9	MCF-7	breast:
16	chr9:101760854..101761829-chr9:101902660..101903198,2	MCF-7	breast:
17	chr9:101759295..101764429-chr9:101866150..101870418,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267026	Chromatin interaction
ENSG00000106799	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10988495	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10988507	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10988510	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10988530	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11515534	0.80[ASN][1000 genomes]
rs12377855	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12378396	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12379014	0.82[JPT][hapmap]
rs12380469	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2416664	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3739799	0.87[JPT][hapmap];0.83[MKK][hapmap]
rs3780622	0.87[JPT][hapmap]
rs56150005	0.94[EUR][1000 genomes]
rs61462449	0.89[ASN][1000 genomes]
rs7022881	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7032060	0.87[JPT][hapmap]
rs7034847	0.87[JPT][hapmap];0.91[MKK][hapmap]
rs7848837	0.87[JPT][hapmap]
rs7851787	0.87[JPT][hapmap]
rs7861925	0.87[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv6635	chr9:101728257-101773253	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10988521	C9orf3	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101754800-101761800	Enhancers	Right Ventricle	heart
2	chr9:101755200-101761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:101755600-101761800	Enhancers	Left Ventricle	heart
4	chr9:101755800-101761800	Enhancers	Rectal Smooth Muscle	rectum
5	chr9:101756000-101761000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:101756400-101761400	Weak transcription	Spleen	Spleen
7	chr9:101757400-101763400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:101758000-101761200	Weak transcription	Colonic Mucosa	Colon
9	chr9:101759000-101761000	Enhancers	Colon Smooth Muscle	Colon
10	chr9:101759000-101762000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:101759200-101761800	Genic enhancers	Fetal Muscle Leg	muscle
12	chr9:101759200-101761800	Genic enhancers	Fetal Stomach	stomach
13	chr9:101759200-101761800	Enhancers	NHDF-Ad	bronchial
14	chr9:101759200-101762000	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr9:101759600-101761600	Enhancers	HSMM	muscle
16	chr9:101759600-101762600	Enhancers	Placenta	Placenta
17	chr9:101759800-101761000	Bivalent Enhancer	NH-A	brain
18	chr9:101759800-101761200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
19	chr9:101759800-101761600	Enhancers	Lung	lung
20	chr9:101759800-101761800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:101759800-101761800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:101759800-101762400	Enhancers	NHLF	lung
23	chr9:101760000-101761000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:101760000-101761000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr9:101760000-101761000	Weak transcription	Hela-S3	cervix
26	chr9:101760000-101761600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:101760000-101761800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr9:101760000-101761800	Enhancers	HSMMtube	muscle
29	chr9:101760200-101761000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr9:101760200-101761200	Weak transcription	Right Atrium	heart
31	chr9:101760200-101761200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:101760200-101762200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr9:101760200-101772800	Weak transcription	Aorta	Aorta
34	chr9:101760400-101761000	Flanking Active TSS	Fetal Heart	heart
35	chr9:101760400-101763000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:101760400-101763000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:101760400-101767400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:101760600-101761000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:101760600-101761200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:101760600-101761200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:101760600-101761200	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr9:101760600-101761600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:101760800-101761000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:101760800-101761000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr9:101760800-101761000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:101760800-101761000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:101760800-101761000	Enhancers	Brain Substantia Nigra	brain
48	chr9:101760800-101761200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:101760800-101761200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr9:101760800-101761200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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