Variant report

Variant	rs17009629
Chromosome Location	chr12:82873850-82873851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10219540	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10431469	0.81[YRI][hapmap]
rs10732677	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10735454	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10735455	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10746242	0.83[YRI][hapmap]
rs10746243	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10746245	0.83[YRI][hapmap]
rs10746247	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10746248	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10746250	0.83[EUR][1000 genomes]
rs10778897	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10778903	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10778905	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs10778906	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10778908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs10862482	0.83[YRI][hapmap]
rs10862484	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10862485	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10862486	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11837949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494023	0.81[YRI][hapmap]
rs1494024	0.83[YRI][hapmap]
rs17009622	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17719033	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17775000	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17775447	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17775501	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17776114	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874058	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes]
rs2068633	0.85[YRI][hapmap]
rs2254688	1.00[CEU][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs2401026	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2401027	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2401032	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2401034	0.81[YRI][hapmap]
rs2401039	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2642010	0.81[YRI][hapmap]
rs2642015	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2642017	0.83[EUR][1000 genomes]
rs2642018	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2642019	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2642023	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2717446	0.81[YRI][hapmap]
rs2717449	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2717459	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2731286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2731288	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2731289	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes]
rs2731290	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2731291	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2731292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2731294	0.89[EUR][1000 genomes]
rs2731295	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2731297	0.81[EUR][1000 genomes]
rs2895910	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2895912	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2895915	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4143187	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41535250	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4242864	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4242870	0.86[YRI][hapmap]
rs4257045	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs4284465	0.83[EUR][1000 genomes]
rs4296098	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4334093	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4343090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4356298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4370996	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4387422	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4399377	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4411333	0.83[YRI][hapmap]
rs4417379	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4505128	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4516038	1.00[CEU][hapmap]
rs4517594	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4540892	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs4553425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4587790	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4628747	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882379	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882386	0.83[EUR][1000 genomes]
rs4882389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4882390	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4882435	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs55806388	0.89[EUR][1000 genomes]
rs55887136	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56337649	0.83[EUR][1000 genomes]
rs7133956	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7297164	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7299307	0.83[EUR][1000 genomes]
rs7299616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7304084	0.83[YRI][hapmap]
rs7311246	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs7313975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7315834	0.85[YRI][hapmap]
rs7316500	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7488252	0.82[YRI][hapmap]
rs7953161	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953234	0.89[EUR][1000 genomes]
rs7954119	1.00[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7954460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7969953	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7971746	0.93[AFR][1000 genomes]
rs7977443	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8181688	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs8181705	1.00[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv1841396	chr12:82768717-82881082	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv519197	chr12:82831845-83056476	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82834000-82874400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:82837800-82876400	Weak transcription	Psoas Muscle	Psoas
3	chr12:82867800-82874400	Weak transcription	Primary B cells from cord blood	blood
4	chr12:82868000-82874600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:82868400-82874000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:82869000-82876000	Weak transcription	Adipose Nuclei	Adipose
7	chr12:82872000-82878200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:82873000-82874000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:82873000-82874000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:82873000-82874200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:82873000-82874800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:82873200-82874000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:82873200-82874000	Enhancers	NHEK	skin
14	chr12:82873200-82874200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:82873200-82874200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:82873200-82876400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:82873600-82874000	Enhancers	NH-A	brain
18	chr12:82873600-82874200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:82873600-82880400	Weak transcription	HUVEC	blood vessel
20	chr12:82873800-82874000	Enhancers	Brain Inferior Temporal Lobe	brain

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