Variant report

Variant	rs12002550
Chromosome Location	chr9:94476418-94476419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94186298..94187810-chr9:94475229..94478202,2	MCF-7	breast:
2	chr9:94474813..94478609-chr9:94479157..94482495,5	K562	blood:
3	chr9:94444042..94444597-chr9:94475780..94476737,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1135150	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1135169	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12004963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2230577	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41308938	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4548304	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56742324	0.84[AFR][1000 genomes]
rs57486734	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7018919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv521046	chr9:94456714-94476418	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv516266	chr9:94458669-94476418	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12002550	AUH	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94458000-94489800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:94469400-94476600	Weak transcription	Colonic Mucosa	Colon
3	chr9:94469400-94476600	Weak transcription	Fetal Stomach	stomach
4	chr9:94472400-94476800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:94472800-94476600	Enhancers	Primary B cells from peripheral blood	blood
6	chr9:94473000-94476600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:94473200-94476600	Weak transcription	Right Atrium	heart
8	chr9:94473800-94483400	Weak transcription	K562	blood
9	chr9:94474200-94476600	Weak transcription	Gastric	stomach
10	chr9:94474200-94476600	Weak transcription	Lung	lung
11	chr9:94474200-94476600	Weak transcription	NH-A	brain
12	chr9:94474200-94480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:94474200-94486000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:94474400-94476600	Weak transcription	Fetal Kidney	kidney
15	chr9:94474400-94476800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:94474400-94477800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:94474600-94476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:94474600-94476600	Weak transcription	Pancreas	Pancrea
19	chr9:94474800-94476600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:94474800-94476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:94474800-94476600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr9:94475200-94476600	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:94475200-94476600	Enhancers	GM12878-XiMat	blood
24	chr9:94475200-94477600	Weak transcription	Brain Germinal Matrix	brain
25	chr9:94475800-94476600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr9:94476000-94476600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr9:94476000-94476600	Enhancers	Fetal Thymus	thymus
28	chr9:94476000-94477000	Enhancers	Primary B cells from cord blood	blood
29	chr9:94476000-94477000	Active TSS	Osteobl	bone
30	chr9:94476000-94477200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:94476000-94477200	Active TSS	A549	lung
32	chr9:94476200-94476600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:94476200-94476600	Enhancers	Fetal Muscle Trunk	muscle
34	chr9:94476200-94476600	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:94476200-94476800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr9:94476200-94477000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:94476200-94477200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr9:94476200-94477200	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr9:94476200-94477200	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr9:94476200-94477200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:94476200-94477400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:94476200-94477800	Active TSS	Stomach Smooth Muscle	stomach
43	chr9:94476400-94476600	Active TSS	Primary hematopoietic stem cells	blood
44	chr9:94476400-94476600	Weak transcription	Fetal Brain Male	brain
45	chr9:94476400-94476800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr9:94476400-94477200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:94476400-94477200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:94476400-94477200	Active TSS	Fetal Intestine Large	intestine
49	chr9:94476400-94477400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:94476400-94478400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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