Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54371813..54373990-chr3:54376911..54378981,2	K562	blood:
2	chr3:54339706..54342583-chr3:54377955..54380864,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs41277447	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55715726	0.82[EUR][1000 genomes]
rs56305246	0.81[EUR][1000 genomes]
rs57711599	0.83[EUR][1000 genomes]
rs60921965	0.82[EUR][1000 genomes]
rs61027914	0.83[EUR][1000 genomes]
rs61566355	0.82[EUR][1000 genomes]
rs62254144	0.82[EUR][1000 genomes]
rs62254148	0.83[EUR][1000 genomes]
rs62254159	0.83[EUR][1000 genomes]
rs62256061	0.85[EUR][1000 genomes]
rs62256085	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256089	0.81[ASN][1000 genomes]
rs62256091	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256099	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6445646	0.94[CEU][hapmap]
rs6769262	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810291	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7428097	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs7434141	0.94[CEU][hapmap];0.83[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7426971	NEK4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54375600-54380000	Weak transcription	Spleen	Spleen
2	chr3:54375600-54382000	Weak transcription	Hela-S3	cervix
3	chr3:54376800-54379800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:54377000-54380400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:54377000-54380600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:54377200-54378600	Weak transcription	Ovary	ovary
7	chr3:54377200-54383200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54377400-54380400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:54377600-54378600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:54377600-54378800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:54377600-54380000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:54377800-54383200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:54378000-54380000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:54378000-54380000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:54378000-54380400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:54378200-54378400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:54378200-54379000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:54378200-54379200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:54378200-54380600	Enhancers	HUES6 Cell Line	embryonic stem cell

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