Variant report

Variant	rs1493408
Chromosome Location	chr12:86628753-86628754
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:86626187..86628759-chr12:86629956..86631967,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10160933	1.00[JPT][hapmap]
rs10776953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776954	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10858412	0.89[CEU][hapmap]
rs11103880	1.00[JPT][hapmap]
rs12309228	1.00[JPT][hapmap]
rs12311272	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12311407	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12311449	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13378062	1.00[JPT][hapmap]
rs1389292	0.84[CEU][hapmap]
rs1389294	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1389295	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1463749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1463750	0.84[CEU][hapmap]
rs1493413	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1493416	0.88[ASN][1000 genomes]
rs1493417	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1493418	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1493419	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1493420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493421	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1532263	0.84[CEU][hapmap]
rs1542780	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1552839	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1602850	0.88[ASN][1000 genomes]
rs1628799	0.83[CEU][hapmap]
rs1689364	0.84[CEU][hapmap]
rs2131565	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2201281	1.00[JPT][hapmap]
rs2250915	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2405934	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2406128	0.89[CEU][hapmap]
rs2452803	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2452805	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2452806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2452811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2452815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2465142	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2465145	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2465146	0.88[ASN][1000 genomes]
rs2465148	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2465149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2471561	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471563	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471564	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2471565	0.83[CEU][hapmap]
rs2471567	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4329741	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6538023	0.81[CEU][hapmap]
rs6538024	0.85[EUR][1000 genomes]
rs7134045	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7137308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7953494	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs839100	0.84[CEU][hapmap]
rs839107	0.84[CEU][hapmap]
rs839147	0.83[CEU][hapmap]
rs839152	0.83[CEU][hapmap]
rs839166	0.94[CEU][hapmap]
rs839183	0.83[CEU][hapmap]
rs844433	0.84[CEU][hapmap]
rs844434	1.00[CEU][hapmap]
rs858213	0.84[CEU][hapmap]
rs863394	0.90[EUR][1000 genomes]

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	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86626400-86629000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:86627400-86629200	Weak transcription	Fetal Heart	heart
3	chr12:86627800-86629400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:86628000-86629400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:86628400-86631600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:86628600-86628800	Enhancers	Brain Germinal Matrix	brain

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