Variant report

No.	Distal block	Cell Line	Cell type
1	chr6:37552277..37554513-chr6:37557977..37561095,3	K562	blood:
2	chr6:37557368..37559370-chr6:37630271..37632684,2	MCF-7	breast:
3	chr6:37544738..37547399-chr6:37555553..37558096,2	MCF-7	breast:
4	chr6:37556006..37559631-chr6:37561589..37564141,4	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1621500	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1738442	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738443	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738444	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1738458	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1776442	0.81[CHB][hapmap]
rs2012000	0.89[ASN][1000 genomes]
rs2395675	0.90[ASN][1000 genomes]
rs2395676	0.90[ASN][1000 genomes]
rs2395677	0.90[ASN][1000 genomes]
rs2746439	0.85[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2797787	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2894413	0.90[ASN][1000 genomes]
rs6458004	0.91[ASN][1000 genomes]
rs6903811	0.83[ASN][1000 genomes]
rs6903990	0.86[ASN][1000 genomes]
rs6904374	0.86[ASN][1000 genomes]
rs6923753	0.86[ASN][1000 genomes]
rs7749225	0.91[ASN][1000 genomes]
rs7753616	0.90[ASN][1000 genomes]
rs7765821	0.85[ASN][1000 genomes]
rs7774871	0.90[ASN][1000 genomes]
rs9394440	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470636	0.90[ASN][1000 genomes]
rs9470637	0.86[ASN][1000 genomes]

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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1776441	LRFN2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37552600-37558600	Enhancers	Fetal Brain Male	brain
2	chr6:37553400-37559400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:37556600-37561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37556600-37562000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:37556600-37567600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:37556800-37558400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:37556800-37559200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:37557200-37558000	Enhancers	Fetal Brain Female	brain
9	chr6:37557200-37558200	Enhancers	Brain Germinal Matrix	brain
10	chr6:37557600-37558000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:37557800-37558400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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