Variant report

Variant	rs10124390
Chromosome Location	chr9:86549939-86549940
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86549593..86551703-chr9:86556254..86557805,2	MCF-7	breast:
2	chr9:86534561..86538761-chr9:86547777..86551990,5	MCF-7	breast:
3	chr9:86548981..86555040-chr9:86588754..86596573,13	MCF-7	breast:
4	chr9:86548960..86550790-chr9:86568981..86570981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178966	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000165119	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10125673	0.95[ASN][1000 genomes]
rs10780639	0.85[EUR][1000 genomes]
rs10780640	0.80[EUR][1000 genomes]
rs10868077	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10868079	0.87[CHB][hapmap]
rs11140240	0.83[CHB][hapmap]
rs11792634	0.81[CHB][hapmap]
rs12349272	0.83[CHB][hapmap]
rs12551039	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs1572030	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572031	0.87[CHB][hapmap]
rs177042	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2065516	0.87[CHB][hapmap]
rs2780142	0.87[CHB][hapmap]
rs295274	0.87[CHB][hapmap]
rs295291	0.83[CHB][hapmap]
rs296885	0.87[CHB][hapmap]
rs296891	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs296892	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3180887	0.82[LWK][hapmap]
rs4297107	0.83[CHB][hapmap]
rs4877814	0.95[CHB][hapmap]
rs4877815	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs5018100	0.87[EUR][1000 genomes]
rs6559750	0.87[CHB][hapmap]
rs6559753	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs6559754	0.86[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs6559756	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs7021189	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7026436	0.82[CHB][hapmap]
rs7045008	0.87[EUR][1000 genomes]
rs754144	0.87[CHB][hapmap]
rs7855503	0.83[CHB][hapmap]
rs7864367	0.83[EUR][1000 genomes]
rs7869387	0.87[CHB][hapmap]
rs7875011	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875242	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875289	0.86[CHB][hapmap]
rs796000	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796001	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796002	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9314723	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10124390	RMI1	cis	parietal	SCAN
rs10124390	C9orf64	cis	cerebellum	SCAN
rs10124390	C9orf64	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
4	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
5	chr9:86544000-86552400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:86545400-86550400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr9:86546400-86550400	Enhancers	Placenta	Placenta
8	chr9:86546800-86553400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr9:86546800-86553600	Weak transcription	Fetal Thymus	thymus
10	chr9:86547200-86553600	Weak transcription	Primary T cells from cord blood	blood
11	chr9:86547200-86553800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:86547800-86554200	Weak transcription	Dnd41	blood
14	chr9:86548000-86550400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
16	chr9:86548400-86550200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:86548600-86550200	Enhancers	Adipose Nuclei	Adipose
18	chr9:86548600-86550200	Enhancers	HUVEC	blood vessel
19	chr9:86548600-86550400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr9:86548600-86550400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:86548600-86550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:86548600-86550800	Enhancers	NHLF	lung
23	chr9:86548600-86551000	Enhancers	HMEC	breast
24	chr9:86548600-86551000	Enhancers	NHEK	skin
25	chr9:86548600-86551200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:86548600-86551800	Enhancers	NHDF-Ad	bronchial
27	chr9:86548600-86551800	Enhancers	Osteobl	bone
28	chr9:86548600-86552000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:86548600-86552600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:86548600-86552600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr9:86548600-86553000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:86548800-86550200	Enhancers	HepG2	liver
33	chr9:86548800-86550400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:86548800-86550600	Enhancers	Psoas Muscle	Psoas
35	chr9:86548800-86554400	Weak transcription	Small Intestine	intestine
36	chr9:86549000-86550200	Enhancers	Primary hematopoietic stem cells	blood
37	chr9:86549000-86550200	Enhancers	A549	lung
38	chr9:86549000-86550200	Flanking Active TSS	Hela-S3	cervix
39	chr9:86549000-86550200	Enhancers	HSMMtube	muscle
40	chr9:86549000-86550400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:86549000-86550800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:86549000-86553800	Weak transcription	Pancreas	Pancrea
43	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:86549200-86550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:86549200-86550000	Weak transcription	Lung	lung
46	chr9:86549200-86550200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr9:86549200-86550800	Enhancers	HSMM	muscle
48	chr9:86549200-86551000	Enhancers	NH-A	brain
49	chr9:86549400-86550800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:86549400-86550800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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