Variant report

Variant	rs7466603
Chromosome Location	chr9:94483198-94483199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10441775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761129	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1201035	0.80[ASN][1000 genomes]
rs2230578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2387996	0.85[ASN][1000 genomes]
rs3121163	0.82[ASN][1000 genomes]
rs4743850	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs56009112	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73521455	0.87[ASN][1000 genomes]
rs73521457	0.90[ASN][1000 genomes]
rs923769	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs923771	0.85[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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7466603	BICD2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94458000-94489800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:94473800-94483400	Weak transcription	K562	blood
3	chr9:94474200-94486000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94476400-94485400	Weak transcription	Fetal Lung	lung
5	chr9:94477000-94483400	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:94477000-94487000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:94477200-94483400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:94477200-94484600	Weak transcription	Ovary	ovary
9	chr9:94477200-94489800	Weak transcription	Right Atrium	heart
10	chr9:94477200-94496800	Weak transcription	NHLF	lung
11	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
12	chr9:94477800-94483200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:94477800-94483800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:94478800-94484400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:94478800-94484600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:94479400-94484400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:94480600-94484400	Weak transcription	Gastric	stomach
18	chr9:94480800-94483400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:94481200-94484400	Weak transcription	Fetal Intestine Small	intestine
20	chr9:94481800-94483800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:94481800-94484000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:94482000-94484400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:94482000-94484400	Weak transcription	Fetal Intestine Large	intestine
24	chr9:94482200-94483600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr9:94482200-94483800	Enhancers	Primary hematopoietic stem cells	blood
26	chr9:94482200-94483800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:94482400-94483800	Enhancers	Primary B cells from cord blood	blood
28	chr9:94482400-94484000	Enhancers	Primary B cells from peripheral blood	blood
29	chr9:94482400-94484400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:94482400-94491600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:94482600-94484200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:94482800-94483200	Flanking Active TSS	GM12878-XiMat	blood
33	chr9:94482800-94483400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:94482800-94484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:94483000-94483200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:94483000-94483200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr9:94483000-94484600	Enhancers	Placenta	Placenta
38	chr9:94483000-94496600	Strong transcription	Fetal Stomach	stomach

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