Variant report

No.	Distal block	Cell Line	Cell type
1	chr1:84541371..84543109-chr1:84583953..84586517,2	K562	blood:
2	chr1:84463824..84465552-chr1:84584447..84586130,2	MCF-7	breast:
3	chr1:84373495..84376180-chr1:84584057..84587374,3	K562	blood:

Variant related genes	Relation type
ENSG00000137941	Chromatin interaction

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10493750	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11163897	0.80[JPT][hapmap]
rs11163898	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11163900	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12070547	0.89[ASN][1000 genomes]
rs12119275	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs12132002	0.89[GIH][hapmap]
rs12132032	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12404263	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12405120	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12746741	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs17099118	0.85[TSI][hapmap]
rs34495740	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35452337	0.87[ASN][1000 genomes]
rs3861699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6669045	0.93[ASN][1000 genomes]
rs6674038	0.80[JPT][hapmap]
rs6703653	0.90[JPT][hapmap]
rs67276144	0.89[ASN][1000 genomes]
rs72711192	0.93[ASN][1000 genomes]
rs7520283	0.90[JPT][hapmap]
rs953197	0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs957828	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12724598	MCOLN2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84569200-84587400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:84569200-84599600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:84569400-84587400	Weak transcription	Ovary	ovary
4	chr1:84574000-84587400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:84574800-84585600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:84576000-84591800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:84582800-84586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:84584000-84587200	Weak transcription	Fetal Heart	heart
9	chr1:84584000-84587400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:84584000-84587400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:84584000-84587800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:84584000-84591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:84584000-84592600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:84584000-84609600	Weak transcription	HSMM	muscle
15	chr1:84584000-84609800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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