Variant report

Variant	rs12469228
Chromosome Location	chr2:186764675-186764676
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	chr2:186760390..186763157-chr2:186764375..186766387,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1010838	0.80[ASN][1000 genomes]
rs1010839	0.81[ASN][1000 genomes]
rs10188205	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190413	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1019428	0.83[ASN][1000 genomes]
rs1019429	0.83[ASN][1000 genomes]
rs1019430	0.83[ASN][1000 genomes]
rs10195661	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210339	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10490390	0.83[ASN][1000 genomes]
rs10490391	0.83[ASN][1000 genomes]
rs10490392	0.83[ASN][1000 genomes]
rs10931198	0.83[ASN][1000 genomes]
rs10931200	0.83[ASN][1000 genomes]
rs10931204	0.83[ASN][1000 genomes]
rs10931205	0.83[ASN][1000 genomes]
rs10931206	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931208	0.87[ASN][1000 genomes]
rs10931210	0.81[ASN][1000 genomes]
rs1119051	0.81[ASN][1000 genomes]
rs11686997	0.83[ASN][1000 genomes]
rs11695215	0.83[ASN][1000 genomes]
rs11695263	0.81[ASN][1000 genomes]
rs11883784	0.83[ASN][1000 genomes]
rs12468672	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615124	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619847	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622494	0.85[ASN][1000 genomes]
rs12623222	0.85[ASN][1000 genomes]
rs12693420	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693422	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13009116	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1386521	0.81[ASN][1000 genomes]
rs1487359	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16827305	0.81[ASN][1000 genomes]
rs16827310	0.81[ASN][1000 genomes]
rs17229201	0.83[ASN][1000 genomes]
rs17229222	0.83[ASN][1000 genomes]
rs1862066	0.83[ASN][1000 genomes]
rs1906235	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2101414	0.81[ASN][1000 genomes]
rs2161035	0.83[ASN][1000 genomes]
rs2161036	0.83[ASN][1000 genomes]
rs2287605	0.83[ASN][1000 genomes]
rs2287606	0.83[ASN][1000 genomes]
rs2370508	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2887762	0.81[ASN][1000 genomes]
rs36004074	0.83[ASN][1000 genomes]
rs4290621	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4349308	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4539761	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4547499	0.83[ASN][1000 genomes]
rs4600604	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4627528	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667063	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55938253	0.83[ASN][1000 genomes]
rs58148758	0.85[ASN][1000 genomes]
rs58798964	0.83[ASN][1000 genomes]
rs60029104	0.83[ASN][1000 genomes]
rs6434144	0.83[ASN][1000 genomes]
rs6705753	0.81[ASN][1000 genomes]
rs6722041	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724942	0.81[ASN][1000 genomes]
rs6725614	0.81[AMR][1000 genomes]
rs6733690	0.81[ASN][1000 genomes]
rs6737654	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6745509	0.88[ASN][1000 genomes]
rs6746722	0.81[ASN][1000 genomes]
rs6756632	0.92[EUR][1000 genomes]
rs72905933	0.81[ASN][1000 genomes]
rs72905952	0.81[ASN][1000 genomes]
rs72905954	0.81[ASN][1000 genomes]
rs7355630	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7355674	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7421273	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572909	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7573074	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7577036	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587008	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7605884	0.83[ASN][1000 genomes]
rs7608481	0.85[ASN][1000 genomes]
rs992822	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1797599	chr2:186618494-186882821	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1002243	chr2:186692815-187150225	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv536077	chr2:186692815-187150225	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv998624	chr2:186735464-186845432	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv584023	chr2:186750735-186851224	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv875546	chr2:186756348-186892254	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12469228	AC007966.1	cis	Nerve Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186716800-186767200	Weak transcription	Ovary	ovary
2	chr2:186764200-186764800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:186764400-186764800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:186764600-186767600	Weak transcription	Psoas Muscle	Psoas

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