Variant report

Variant	rs7046900
Chromosome Location	chr9:97713098-97713099
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97687410..97690571-chr9:97710837..97713862,3	MCF-7	breast:
2	chr9:97705028..97708373-chr9:97712874..97716107,3	MCF-7	breast:
3	chr9:97711544..97713336-chr9:97713597..97715255,2	MCF-7	breast:
4	chr9:97544875..97545760-chr9:97712980..97713877,4	MCF-7	breast:
5	chr9:97712288..97714275-chr9:97755356..97757611,2	MCF-7	breast:
6	chr9:97711965..97713605-chr9:97715460..97717301,2	MCF-7	breast:
7	chr9:97712076..97713650-chr9:97766495..97769032,2	MCF-7	breast:
8	chr9:97712985..97713881-chr9:97754020..97754788,2	MCF-7	breast:
9	chr9:97711689..97714649-chr9:97733547..97735329,2	MCF-7	breast:
10	chr9:97712915..97713959-chr9:97753956..97754999,6	MCF-7	breast:
11	chr9:97712961..97713959-chr9:97754003..97754999,3	MCF-7	breast:
12	chr9:97544875..97545769-chr9:97712980..97713877,6	MCF-7	breast:
13	chr9:97544841..97545856-chr9:97712881..97713857,5	MCF-7	breast:
14	chr9:97711176..97714022-chr9:97766697..97771903,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10125566	0.84[AMR][1000 genomes]
rs1020962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217441	0.84[AMR][1000 genomes]
rs1038092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10732407	0.84[AMR][1000 genomes]
rs10739988	0.84[AMR][1000 genomes]
rs10739990	0.84[AMR][1000 genomes]
rs10761362	0.81[AMR][1000 genomes]
rs10761371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10821411	0.84[AMR][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1113967	0.84[AMR][1000 genomes]
rs12551506	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12552838	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12554043	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12554454	0.82[EUR][1000 genomes]
rs12555128	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12555829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12683896	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1382411	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1382412	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1542107	0.84[AMR][1000 genomes]
rs1564235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1571896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap]
rs16911834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16911856	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs16911862	0.86[EUR][1000 genomes]
rs1871220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1888944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1888945	0.93[ASN][1000 genomes]
rs1888946	0.93[ASN][1000 genomes]
rs1904201	0.97[AMR][1000 genomes]
rs2026399	0.97[AMR][1000 genomes]
rs2061798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2061801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2095069	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2104888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2119953	0.84[AMR][1000 genomes]
rs2306207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2406897	0.84[AMR][1000 genomes]
rs2406898	0.84[AMR][1000 genomes]
rs2897523	0.84[AMR][1000 genomes]
rs35322834	0.86[EUR][1000 genomes]
rs3739748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap]
rs3847311	0.81[AMR][1000 genomes]
rs3886568	0.84[AMR][1000 genomes]
rs41316526	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4332191	0.84[AMR][1000 genomes]
rs4743975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743978	0.93[ASN][1000 genomes]
rs4743989	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4744389	0.84[AMR][1000 genomes]
rs4744421	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744429	0.93[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6479581	0.84[AMR][1000 genomes]
rs66642068	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66863985	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66993340	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs67490803	1.00[AMR][1000 genomes]
rs67756624	0.88[AMR][1000 genomes]
rs7019602	0.84[AMR][1000 genomes]
rs7022963	1.00[JPT][hapmap]
rs7029570	0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039768	0.93[ASN][1000 genomes]
rs7044371	0.84[AMR][1000 genomes]
rs72748596	0.86[EUR][1000 genomes]
rs72748601	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72750335	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72750346	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72750351	0.96[ASN][1000 genomes]
rs72750359	0.96[ASN][1000 genomes]
rs72750367	0.93[ASN][1000 genomes]
rs72750373	0.93[ASN][1000 genomes]
rs73538177	0.88[AMR][1000 genomes]
rs73540087	0.93[ASN][1000 genomes]
rs7869736	0.84[AMR][1000 genomes]
rs894426	0.84[AMR][1000 genomes]
rs894427	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7046900	C9orf3	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97682000-97713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:97687000-97714000	Weak transcription	Thymus	Thymus
5	chr9:97700200-97714600	Weak transcription	Fetal Stomach	stomach
6	chr9:97700200-97718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:97707000-97713400	Weak transcription	Small Intestine	intestine
8	chr9:97707800-97713200	Enhancers	Aorta	Aorta
9	chr9:97708200-97713200	Enhancers	A549	lung
10	chr9:97708800-97713200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:97708800-97713200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:97708800-97714000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:97708800-97715000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:97708800-97720000	Weak transcription	K562	blood
15	chr9:97709200-97713400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:97709200-97730400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:97709600-97713200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:97709600-97713600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr9:97709800-97713800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr9:97709800-97713800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr9:97710000-97713600	Enhancers	Brain Angular Gyrus	brain
22	chr9:97710000-97713600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:97710000-97715200	Enhancers	Ovary	ovary
24	chr9:97710000-97715600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:97710400-97715000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:97710600-97713400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:97710600-97716000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr9:97710600-97716200	Enhancers	Left Ventricle	heart
29	chr9:97710600-97716800	Enhancers	Placenta	Placenta
30	chr9:97710800-97713400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr9:97710800-97713400	Enhancers	Fetal Heart	heart
32	chr9:97710800-97713800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:97710800-97714200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr9:97710800-97715600	Genic enhancers	HSMM	muscle
35	chr9:97711000-97713400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr9:97711200-97715800	Enhancers	Brain Anterior Caudate	brain
37	chr9:97711200-97715800	Enhancers	Brain Substantia Nigra	brain
38	chr9:97711200-97716200	Enhancers	Fetal Muscle Leg	muscle
39	chr9:97711200-97719000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:97711400-97713200	Weak transcription	HMEC	breast
41	chr9:97711400-97714600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:97711400-97714800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:97711400-97717400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:97711600-97715800	Enhancers	Brain Hippocampus Middle	brain
45	chr9:97711800-97714600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:97711800-97715800	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:97711800-97716800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:97712000-97715400	Enhancers	Right Ventricle	heart
49	chr9:97712000-97716000	Enhancers	HSMMtube	muscle
50	chr9:97712200-97715600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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