Variant report

Variant	rs2404458
Chromosome Location	chr9:97933023-97933024
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	chr9:97910896..97912573-chr9:97931774..97933333,2	K562	blood:
2	chr9:97928874..97931668-chr9:97931897..97933841,2	K562	blood:

Variant related genes	Relation type
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1004813	0.88[GIH][hapmap]
rs12683030	0.85[JPT][hapmap]
rs12683182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1875835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1886993	1.00[ASN][1000 genomes]
rs2121200	1.00[ASN][1000 genomes]
rs35108112	1.00[ASN][1000 genomes]
rs3780566	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3802449	0.85[JPT][hapmap]
rs400727	0.85[JPT][hapmap]
rs4647348	0.89[ASN][1000 genomes]
rs4647352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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	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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647405	1.00[ASN][1000 genomes]
rs4647408	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647430	0.87[AFR][1000 genomes];1.00[AMR][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]
rs4647464	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647465	1.00[ASN][1000 genomes]
rs4647466	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647474	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647477	1.00[ASN][1000 genomes]
rs4647484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647485	1.00[ASN][1000 genomes]
rs4647486	1.00[ASN][1000 genomes]
rs4647487	0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647493	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647502	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647508	1.00[ASN][1000 genomes]
rs4647509	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4647510	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4647514	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4647516	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4647521	0.88[ASN][1000 genomes]
rs4647549	0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs57641389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60228132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61358915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7037729	1.00[ASN][1000 genomes]
rs73528484	1.00[AFR][1000 genomes]
rs73528487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73530498	1.00[ASN][1000 genomes]
rs73532103	1.00[ASN][1000 genomes]
rs73534874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534875	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534887	1.00[ASN][1000 genomes]
rs73534888	1.00[ASN][1000 genomes]
rs73534896	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73534898	1.00[ASN][1000 genomes]
rs73539228	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73539285	1.00[AMR][1000 genomes]
rs7854840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859625	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9792415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792481	1.00[ASN][1000 genomes]
rs9792533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9792691	1.00[ASN][1000 genomes]

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	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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
2	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
4	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
5	chr9:97920400-97951800	Weak transcription	HepG2	liver
6	chr9:97920600-97933400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:97925800-97938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:97925800-97944800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:97926000-97937800	Weak transcription	Psoas Muscle	Psoas
10	chr9:97926400-97934400	Weak transcription	Primary B cells from cord blood	blood
11	chr9:97926800-97933200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:97927600-97950400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:97928600-97933200	Weak transcription	NHEK	skin
14	chr9:97930000-97945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:97930000-97945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:97930600-97933200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:97930600-97939400	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:97930600-97943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:97930600-97944800	Weak transcription	Lung	lung
20	chr9:97930600-97950400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:97930600-97950800	Weak transcription	Thymus	Thymus
22	chr9:97930600-97952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:97930800-97933200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:97930800-97933200	Weak transcription	Osteobl	bone
25	chr9:97930800-97933600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr9:97930800-97940400	Weak transcription	Fetal Thymus	thymus
27	chr9:97930800-97941600	Weak transcription	Liver	Liver
28	chr9:97930800-97951600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:97931000-97933800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:97931200-97937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:97931200-97940000	Weak transcription	Fetal Intestine Small	intestine
33	chr9:97931800-97933200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr9:97931800-97937800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:97932000-97934000	Enhancers	Fetal Heart	heart
36	chr9:97932000-97935000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr9:97932200-97933200	Weak transcription	K562	blood
38	chr9:97932200-97933800	Weak transcription	Dnd41	blood
39	chr9:97932200-97944800	Weak transcription	Primary T cells from cord blood	blood
40	chr9:97932200-97945000	Weak transcription	Fetal Intestine Large	intestine
41	chr9:97932600-97933800	Enhancers	Fetal Lung	lung
42	chr9:97932600-97934200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:97932800-97933200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:97932800-97933400	Enhancers	Stomach Smooth Muscle	stomach
45	chr9:97932800-97933600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:97932800-97933800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr9:97932800-97934000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:97932800-97934200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr9:97932800-97934200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:97932800-97934200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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