Variant report

Variant	rs9426889
Chromosome Location	chr1:170033283-170033284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:170032663..170035514-chr1:170040847..170042460,2	MCF-7	breast:
2	chr1:170030478..170033349-chr1:170042564..170044443,2	K562	blood:
3	chr1:170032070..170034334-chr1:170034537..170036782,2	K562	blood:

Variant related genes	Relation type
ENSG00000075945	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10127867	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023275	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12563479	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12724797	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12739975	0.80[CEU][hapmap]
rs1330372	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361088	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862933	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1765696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2152831	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2273458	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2750014	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2806386	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs33943686	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141917	0.88[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656203	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574211	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673712	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697581	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7418815	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs824668	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9426889	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:169999800-170036600	Weak transcription	Small Intestine	intestine
3	chr1:170002800-170036400	Weak transcription	NHDF-Ad	bronchial
4	chr1:170018200-170042400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:170018600-170035800	Weak transcription	Liver	Liver
6	chr1:170018800-170034600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:170018800-170037000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:170018800-170040600	Weak transcription	Aorta	Aorta
9	chr1:170019000-170035600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:170019000-170037000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:170019000-170041400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:170019000-170042600	Weak transcription	Thymus	Thymus
13	chr1:170019200-170036800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:170019200-170042400	Weak transcription	Fetal Lung	lung
15	chr1:170024000-170036400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:170024400-170037800	Weak transcription	Primary T cells from cord blood	blood
17	chr1:170024600-170036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:170027800-170036600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:170031400-170033800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:170031800-170033600	Enhancers	HMEC	breast
21	chr1:170032600-170033800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:170032600-170036600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:170032600-170036600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:170032800-170033400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:170032800-170033400	Weak transcription	Brain Germinal Matrix	brain
26	chr1:170032800-170035600	Weak transcription	K562	blood
27	chr1:170032800-170035800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:170032800-170035800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:170032800-170036400	Weak transcription	Psoas Muscle	Psoas
30	chr1:170032800-170036600	Weak transcription	Left Ventricle	heart
31	chr1:170032800-170036600	Weak transcription	Ovary	ovary
32	chr1:170032800-170037000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:170032800-170040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:170032800-170042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:170032800-170042600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:170033000-170033600	Enhancers	NHEK	skin
37	chr1:170033000-170034200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:170033000-170035600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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