Variant report

Variant	rs12027839
Chromosome Location	chr1:180517505-180517506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180516263..180518210-chr1:180520202..180523252,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10914021	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10914022	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10914035	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10914038	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12027878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045365	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12407684	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1416822	0.85[EUR][1000 genomes]
rs16856127	0.95[EUR][1000 genomes]
rs17300712	0.83[EUR][1000 genomes]
rs4446932	0.83[EUR][1000 genomes]
rs4652509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57537558	0.83[EUR][1000 genomes]
rs58047798	0.83[EUR][1000 genomes]
rs58089956	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60927564	0.82[EUR][1000 genomes]
rs61388681	0.83[EUR][1000 genomes]
rs6425643	0.81[EUR][1000 genomes]
rs6425646	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6694454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72720914	0.83[EUR][1000 genomes]
rs7512134	0.87[ASN][1000 genomes]
rs7525689	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547266	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs946636	0.83[EUR][1000 genomes]
rs961162	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:180511800-180521200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:180512200-180521200	Weak transcription	HSMMtube	muscle
4	chr1:180512400-180517800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:180512800-180517600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:180513000-180518000	Weak transcription	Fetal Brain Male	brain
7	chr1:180513600-180521200	Weak transcription	Right Ventricle	heart
8	chr1:180515000-180518600	Enhancers	Fetal Heart	heart
9	chr1:180515400-180517600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:180516200-180518400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:180516200-180519000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:180516200-180519400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:180516400-180520600	Weak transcription	Left Ventricle	heart
14	chr1:180516400-180521200	Weak transcription	Right Atrium	heart
15	chr1:180516600-180536800	Weak transcription	Psoas Muscle	Psoas
16	chr1:180517200-180517600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:180517200-180519400	Enhancers	Fetal Brain Female	brain
18	chr1:180517400-180518600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:180517400-180519200	Enhancers	Cortex derived primary cultured neurospheres	brain

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