Variant report

Variant	rs12562379
Chromosome Location	chr1:72337425-72337426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11209852	0.83[CHB][hapmap]
rs11209853	0.81[CHB][hapmap]
rs11209857	0.81[ASN][1000 genomes]
rs11209861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11209863	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11209865	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11209867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11579239	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12025922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027233	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12039773	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12042645	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12045130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12046440	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12749167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749550	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1426179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091869	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17091894	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1814055	0.82[CHB][hapmap]
rs35285032	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474680	0.82[EUR][1000 genomes]
rs516876	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs517762	0.82[CHB][hapmap]
rs554161	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs626185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs628247	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs629079	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs648556	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6659202	0.83[CHB][hapmap]
rs6660086	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6683443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700176	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67094512	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv870762	chr1:72300968-72376262	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv871908	chr1:72315820-72370014	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	nsv999162	chr1:72319163-72477496	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv534995	chr1:72319163-72477496	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72336600-72339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:72337400-72339400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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