Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39119197..39119961-chr4:124736001..124736518,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236354	Chromatin interaction

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1016592	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13129313	1.00[CEU][hapmap]
rs1433218	0.81[EUR][1000 genomes]
rs1991839	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2390590	0.83[ASN][1000 genomes]
rs3097909	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097910	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097915	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3097916	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3097917	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3097918	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3097919	0.87[EUR][1000 genomes]
rs3097920	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3097925	0.81[EUR][1000 genomes]
rs3113362	0.81[EUR][1000 genomes]
rs3113385	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113396	0.87[CHD][hapmap];0.82[MEX][hapmap]
rs6840618	1.00[CEU][hapmap]
rs721456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654237	1.00[CEU][hapmap]
rs7699221	0.96[CEU][hapmap]
rs978534	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
3	esv3516000	chr4:124735925-124736156	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3516001	chr4:124735925-124736156	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3097913	TNIP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124731600-124741000	Weak transcription	Fetal Intestine Small	intestine
2	chr4:124733400-124737200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:124733400-124737600	Weak transcription	NHLF	lung
4	chr4:124733600-124737400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:124733600-124737400	Weak transcription	NHDF-Ad	bronchial
6	chr4:124733600-124737800	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:124733600-124737800	Weak transcription	HSMMtube	muscle
8	chr4:124733600-124738200	Weak transcription	Primary B cells from cord blood	blood
9	chr4:124733600-124738200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:124733800-124737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:124733800-124738200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr4:124734600-124736600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:124735200-124753800	Weak transcription	Psoas Muscle	Psoas
14	chr4:124735600-124737400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:124736000-124736200	Enhancers	Aorta	Aorta

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