Variant report

Variant	rs7854840
Chromosome Location	chr9:97899587-97899588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97898268..97900178-chr9:97902797..97905097,2	K562	blood:
2	chr9:97898732..97900344-chr9:97906581..97908962,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf3-3	chr9:97899455-97899658	NONHSAT133359
2	lnc-C9orf3-3	chr9:97899455-97899658	ucscGeneNc_uc004avy_2

Variant related genes	Relation type
ENSG00000251884	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12683030	0.86[JPT][hapmap]
rs12683182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12684215	1.00[ASN][1000 genomes]
rs12685903	1.00[ASN][1000 genomes]
rs12686588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1800360	0.83[AMR][1000 genomes]
rs1875835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1886993	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2121200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2404458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35108112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3780566	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3802449	0.86[JPT][hapmap]
rs400727	0.86[JPT][hapmap]
rs4647348	0.89[ASN][1000 genomes]
rs4647352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647386	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4647387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647397	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647398	1.00[ASN][1000 genomes]
rs4647402	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647405	1.00[ASN][1000 genomes]
rs4647408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647437	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647449	1.00[ASN][1000 genomes]
rs4647455	0.83[AMR][1000 genomes]
rs4647465	1.00[ASN][1000 genomes]
rs4647466	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4647477	1.00[ASN][1000 genomes]
rs4647484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647485	1.00[ASN][1000 genomes]
rs4647486	1.00[ASN][1000 genomes]
rs4647491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647493	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647505	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647508	1.00[ASN][1000 genomes]
rs4647509	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647514	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647521	0.88[ASN][1000 genomes]
rs4647549	0.85[JPT][hapmap]
rs57471585	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60228132	1.00[ASN][1000 genomes]
rs7034939	0.83[AMR][1000 genomes]
rs7037729	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73528466	0.83[AMR][1000 genomes]
rs73528478	0.83[AMR][1000 genomes]
rs73530498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73532103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73532167	0.83[AMR][1000 genomes]
rs73532195	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73532199	0.83[AMR][1000 genomes]
rs73534887	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73534888	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73534896	0.89[ASN][1000 genomes]
rs73534898	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73537212	0.83[AMR][1000 genomes]
rs73538039	0.83[AMR][1000 genomes]
rs73539203	0.83[AMR][1000 genomes]
rs73541330	0.83[AMR][1000 genomes]
rs9792415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9792533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792691	1.00[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	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	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
3	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
5	chr9:97888000-97900000	Weak transcription	Primary T cells from cord blood	blood
6	chr9:97890000-97900000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
8	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
9	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:97890200-97900400	Weak transcription	Esophagus	oesophagus
11	chr9:97890400-97902800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:97890600-97900000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:97890600-97900000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:97892600-97900400	Weak transcription	Brain Germinal Matrix	brain
15	chr9:97893200-97901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:97893800-97904800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:97893800-97905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:97893800-97905800	Weak transcription	Osteobl	bone
19	chr9:97893800-97906400	Weak transcription	Ovary	ovary
20	chr9:97893800-97912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97893800-97918800	Weak transcription	Gastric	stomach
22	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
23	chr9:97894200-97906200	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:97894200-97909800	Weak transcription	A549	lung
25	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:97894600-97905000	Weak transcription	Fetal Lung	lung
27	chr9:97894800-97905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:97895000-97900200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:97895600-97899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:97895600-97901000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:97895800-97900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:97895800-97903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:97896000-97900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:97896000-97900600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:97896000-97909800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:97896400-97910200	Weak transcription	Small Intestine	intestine
37	chr9:97896400-97918400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:97896400-97920000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:97896600-97905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:97896800-97900600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:97897000-97910000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:97897200-97900000	Weak transcription	Fetal Stomach	stomach
43	chr9:97897200-97900000	Weak transcription	Lung	lung
44	chr9:97897200-97900200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:97897200-97900200	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:97897200-97900400	Weak transcription	Fetal Intestine Large	intestine
47	chr9:97897200-97901600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:97897200-97905000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr9:97897200-97905800	Weak transcription	HepG2	liver
50	chr9:97897200-97917400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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