Variant report

Variant	rs13656
Chromosome Location	chr12:30868002-30868003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1054426	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10734791	0.93[ASN][1000 genomes]
rs10743727	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10743728	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10743733	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743734	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771747	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs10771748	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10771750	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs10771752	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10771754	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771755	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10771758	0.89[ASN][1000 genomes]
rs10771759	0.93[ASN][1000 genomes]
rs10771764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771769	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843796	0.92[CHB][hapmap];0.86[YRI][hapmap]
rs10843799	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs10843806	0.81[ASN][1000 genomes]
rs10843807	0.81[ASN][1000 genomes]
rs10843808	0.81[ASN][1000 genomes]
rs10843809	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10843810	0.92[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10843811	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10843812	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11051013	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11051052	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12370429	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12579337	0.81[ASN][1000 genomes]
rs1371049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371053	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14139	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs1545175	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1866416	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2043846	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2099661	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278558	0.85[JPT][hapmap]
rs2289300	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2289301	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304626	0.81[ASN][1000 genomes]
rs2304630	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2352210	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2352217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33132	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782685	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3816169	0.81[ASN][1000 genomes]
rs3825307	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3910561	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3910564	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4082413	0.86[YRI][hapmap]
rs4143103	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4143104	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4143105	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4930935	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930936	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931356	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60452057	0.80[ASN][1000 genomes]
rs6487925	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6487927	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6487930	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6487932	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487933	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7136079	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs718368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297455	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7298007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298180	0.96[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7304879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304976	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7311651	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315693	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7315932	0.81[ASN][1000 genomes]
rs7316477	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7325	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs7326	0.92[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs7327	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs794152	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7955420	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7955574	0.81[ASN][1000 genomes]
rs7963494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968343	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7968587	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7978343	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7978936	0.81[ASN][1000 genomes]
rs8414	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs9300199	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13656	IPO8	cis	multi-tissue	Pritchard
rs13656	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30849200-30881600	Weak transcription	Right Ventricle	heart
2	chr12:30849600-30881200	Weak transcription	Psoas Muscle	Psoas
3	chr12:30849600-30881600	Weak transcription	Aorta	Aorta
4	chr12:30857400-30881800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:30858000-30891800	Weak transcription	Fetal Heart	heart
6	chr12:30858800-30868600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:30859000-30869400	Weak transcription	K562	blood
8	chr12:30859200-30892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:30859400-30883400	Weak transcription	Colonic Mucosa	Colon
10	chr12:30859800-30877000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:30860200-30871200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:30860400-30881600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:30861000-30879000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:30861200-30871400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:30861200-30875000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:30861400-30869800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:30861400-30872600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:30861400-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:30861400-30885000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
22	chr12:30861800-30869800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:30861800-30870000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:30861800-30872000	Strong transcription	HSMM	muscle
25	chr12:30861800-30872600	Strong transcription	Fetal Brain Female	brain
26	chr12:30861800-30872800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:30861800-30877800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:30861800-30879000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:30861800-30884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:30861800-30894600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:30861800-30895200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:30862000-30869600	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:30862000-30871800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:30862000-30872200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:30862000-30872600	Strong transcription	Liver	Liver
36	chr12:30862000-30877800	Strong transcription	HMEC	breast
37	chr12:30862000-30878800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:30862000-30879000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:30862200-30872200	Strong transcription	Brain Anterior Caudate	brain
40	chr12:30862200-30879000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:30862200-30895000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:30862400-30871000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:30862400-30871200	Strong transcription	Adipose Nuclei	Adipose
44	chr12:30862400-30872000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:30862400-30872400	Strong transcription	Primary T cells from cord blood	blood
46	chr12:30862400-30876600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:30862400-30895600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:30862600-30870400	Strong transcription	A549	lung
49	chr12:30862600-30872400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:30862600-30872400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links