Variant report

Variant	rs12142457
Chromosome Location	chr1:179795463-179795464
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179793280..179795680-chr1:179799049..179800852,2	K562	blood:
2	chr1:179792919..179795470-chr1:179832421..179835252,2	K562	blood:
3	chr1:179794929..179797401-chr1:179800739..179802497,2	MCF-7	breast:
4	chr1:179795002..179797734-chr1:179802507..179804138,2	MCF-7	breast:
5	chr1:179794600..179795490-chr6:105142707..105143333,2	MCF-7	breast:
6	chr1:179794231..179796736-chr1:179797450..179799021,2	K562	blood:

Variant related genes	Relation type
ENSG00000258664	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1048418	1.00[CHB][hapmap]
rs10494523	1.00[CHB][hapmap]
rs10913892	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913905	1.00[CHB][hapmap]
rs10913909	1.00[CHB][hapmap]
rs11590974	1.00[CHB][hapmap]
rs12118565	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119431	1.00[CHB][hapmap]
rs12131200	1.00[CHB][hapmap]
rs12136091	1.00[CHB][hapmap]
rs12136465	1.00[CHB][hapmap]
rs12141134	1.00[CHB][hapmap]
rs12142611	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143942	1.00[CHB][hapmap]
rs12144346	1.00[CHB][hapmap]
rs12144352	1.00[CHB][hapmap]
rs12723969	1.00[CHB][hapmap]
rs12756362	1.00[CHB][hapmap]
rs16854910	1.00[CHB][hapmap]
rs17299006	1.00[CHB][hapmap]
rs17370139	1.00[CHB][hapmap]
rs17371159	1.00[CHB][hapmap]
rs3845388	1.00[CHB][hapmap]
rs4301600	1.00[CHB][hapmap]
rs7518566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531195	1.00[CHB][hapmap]
rs7540487	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv519307	chr1:179766086-179795505	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179791000-179807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179793200-179795600	Enhancers	Fetal Muscle Trunk	muscle
3	chr1:179793400-179795600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:179793400-179796000	Enhancers	Fetal Thymus	thymus
5	chr1:179793800-179796800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:179793800-179808800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:179794000-179796400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:179794400-179795600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:179794400-179795600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:179794400-179795600	Enhancers	Lung	lung
11	chr1:179794600-179804800	Weak transcription	Right Ventricle	heart
12	chr1:179794800-179809200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:179795000-179796000	Enhancers	Spleen	Spleen
14	chr1:179795200-179795600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:179795200-179796000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:179795200-179796200	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr1:179795200-179812400	Weak transcription	Left Ventricle	heart
18	chr1:179795200-179815200	Weak transcription	Ovary	ovary
19	chr1:179795400-179804600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:179795400-179804800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:179795400-179805000	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:179795400-179807600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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