Variant report

Variant	rs9460
Chromosome Location	chr15:73044575-73044576
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	chr15:73042845..73045045-chr15:73109930..73111869,2	MCF-7	breast:
2	chr15:73041118..73044683-chr15:73044703..73047374,3	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	ADPGK	hsa-miR-1	chr15:73044557-73044578

Variant related genes	Relation type
ADPGK	miRNA target site

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10459647	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072385	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631214	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631352	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637168	0.84[ASN][1000 genomes]
rs12900863	0.86[ASN][1000 genomes]
rs12911743	0.81[ASN][1000 genomes]
rs2162269	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2277598	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28582982	0.98[ASN][1000 genomes]
rs34117151	0.86[ASN][1000 genomes]
rs34661924	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3850986	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4776613	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4776614	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4777532	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4777534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs4777536	1.00[ASN][1000 genomes]
rs4777542	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4777546	0.81[ASN][1000 genomes]
rs55914134	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62017600	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495015	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7164727	0.86[ASN][1000 genomes]
rs7166595	0.86[ASN][1000 genomes]
rs7167076	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7171728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7176223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176235	0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7178130	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8024986	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025333	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8030477	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8031455	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8033073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033580	0.95[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8038247	0.86[ASN][1000 genomes]
rs890354	0.84[ASN][1000 genomes]
rs998020	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9460	ARIH1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73002000-73054600	Weak transcription	Fetal Brain Male	brain
2	chr15:73024400-73046800	Weak transcription	Fetal Kidney	kidney
3	chr15:73030000-73044600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:73030400-73046000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:73030600-73058400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:73031000-73044800	Weak transcription	K562	blood
7	chr15:73031400-73044600	Weak transcription	Ovary	ovary
8	chr15:73031600-73045000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:73032800-73044600	Weak transcription	Psoas Muscle	Psoas
10	chr15:73033400-73044600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:73033600-73044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:73033600-73047200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:73034000-73044800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:73034200-73044600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:73035800-73050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:73038800-73044600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:73041600-73047600	Weak transcription	Stomach Mucosa	stomach
18	chr15:73041600-73049800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:73041800-73049000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:73041800-73071000	Strong transcription	Liver	Liver
21	chr15:73042000-73048000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:73042200-73044600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr15:73042200-73044800	Strong transcription	Placenta	Placenta
24	chr15:73042200-73045800	Strong transcription	Rectal Smooth Muscle	rectum
25	chr15:73042200-73048800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:73042200-73049000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:73042200-73053800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:73042200-73055400	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:73042200-73056200	Strong transcription	Thymus	Thymus
30	chr15:73042200-73058600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:73042200-73058600	Strong transcription	A549	lung
32	chr15:73042400-73049000	Strong transcription	Osteobl	bone
33	chr15:73042600-73045200	Strong transcription	NHDF-Ad	bronchial
34	chr15:73042800-73050000	Strong transcription	HSMM	muscle
35	chr15:73043000-73044600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr15:73043000-73044600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:73043200-73044600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:73043200-73044800	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:73043200-73050400	Strong transcription	Colonic Mucosa	Colon
40	chr15:73043200-73053400	Strong transcription	GM12878-XiMat	blood
41	chr15:73043200-73053800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:73043400-73044600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:73043400-73044800	Strong transcription	Lung	lung
44	chr15:73043400-73044800	Strong transcription	Spleen	Spleen
45	chr15:73043400-73045000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:73043400-73045000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:73043400-73045600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr15:73043400-73046000	Strong transcription	NHEK	skin
49	chr15:73043400-73048400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr15:73043400-73048600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links