Variant report

Variant	rs12739715
Chromosome Location	chr1:212596314-212596315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212587042..212589735-chr1:212595320..212598390,3	K562	blood:
2	chr1:212596005..212598294-chr1:212604607..212607533,3	K562	blood:
3	chr1:212587807..212590327-chr1:212593131..212596820,3	K562	blood:

Variant related genes	Relation type
ENSG00000117691	Chromatin interaction
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10157725	1.00[ASN][1000 genomes]
rs1126526	1.00[CHB][hapmap]
rs11803526	1.00[ASN][1000 genomes]
rs11803766	0.99[EUR][1000 genomes]
rs12755383	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17018997	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17019266	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17019397	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2007776	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3001261	1.00[ASN][1000 genomes]
rs35030678	1.00[ASN][1000 genomes]
rs35702733	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35822123	0.82[EUR][1000 genomes]
rs4336916	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4540733	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs492231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs498564	1.00[ASN][1000 genomes]
rs536040	1.00[CHB][hapmap]
rs56085986	1.00[ASN][1000 genomes]
rs58972361	1.00[ASN][1000 genomes]
rs593750	1.00[ASN][1000 genomes]
rs61331273	1.00[ASN][1000 genomes]
rs641053	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs648577	1.00[ASN][1000 genomes]
rs6656320	1.00[ASN][1000 genomes]
rs6666415	0.99[EUR][1000 genomes]
rs6669027	0.95[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6680374	1.00[ASN][1000 genomes]
rs6687793	1.00[ASN][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6697910	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6704234	0.98[EUR][1000 genomes]
rs71646158	0.82[EUR][1000 genomes]
rs71646159	0.93[EUR][1000 genomes]
rs71646161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138106	1.00[ASN][1000 genomes]
rs74138110	1.00[ASN][1000 genomes]
rs74138553	1.00[ASN][1000 genomes]
rs74138559	1.00[ASN][1000 genomes]
rs74140412	1.00[ASN][1000 genomes]
rs7515005	1.00[ASN][1000 genomes]
rs7530106	1.00[ASN][1000 genomes]
rs7533689	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7533954	1.00[ASN][1000 genomes]
rs7537172	1.00[ASN][1000 genomes]
rs7538315	1.00[ASN][1000 genomes]
rs7549085	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7551910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429888	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12739715	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs12739715	RP11-15I11.3	cis	lung	GTEx
rs12739715	RP11-15I11.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212591000-212605600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:212591400-212597800	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:212595200-212598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:212595400-212597600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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