Variant report

Variant	rs12022349
Chromosome Location	chr1:152854193-152854194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11205127	1.00[CEU][hapmap]
rs11205128	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11205129	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];0.96[ASN][1000 genomes]
rs11205131	1.00[JPT][hapmap]
rs11801996	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];0.96[ASN][1000 genomes]
rs12021601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12022319	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12022870	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12026193	1.00[CEU][hapmap]
rs12028228	0.81[ASN][1000 genomes]
rs12047888	0.94[ASN][1000 genomes]
rs12048655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12239808	0.95[JPT][hapmap]
rs12239812	0.91[JPT][hapmap]
rs12239814	0.95[JPT][hapmap]
rs12568299	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs16834715	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16834728	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs16834734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16834746	0.95[JPT][hapmap]
rs2339383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2339398	1.00[CEU][hapmap]
rs2879485	0.95[JPT][hapmap]
rs3737861	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs3737862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4240862	1.00[CEU][hapmap]
rs4363387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4845489	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4845490	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4845491	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4845492	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4845494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60566199	0.96[ASN][1000 genomes]
rs73006590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7542656	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7553755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7556490	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][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	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152853200-152855600	Weak transcription	Esophagus	oesophagus
2	chr1:152853600-152854200	Enhancers	GM12878-XiMat	blood
3	chr1:152853600-152855600	Weak transcription	Ovary	ovary
4	chr1:152853600-152857800	Weak transcription	Liver	Liver
5	chr1:152853800-152855600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:152853800-152855600	Weak transcription	HMEC	breast
7	chr1:152853800-152856000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:152853800-152856000	Weak transcription	NHEK	skin
9	chr1:152853800-152856200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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