Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr12:31797207-31797990	A549	lung:	n/a	chr12:31797386-31797400

Variant related genes	Relation type
METTL20	TF binding region

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12820589	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12820981	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961226	0.84[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10743762	PTHLH	cis	cerebellum	SCAN
rs10743762	REP15	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31783400-31803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:31783400-31803000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:31789600-31803000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:31789800-31801200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:31789800-31803000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:31794800-31799800	Weak transcription	Fetal Kidney	kidney
7	chr12:31795400-31798000	Weak transcription	HepG2	liver
8	chr12:31797000-31800000	Enhancers	Hela-S3	cervix
9	chr12:31797200-31798000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:31797200-31798000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:31797200-31798400	Enhancers	Pancreas	Pancrea
12	chr12:31797200-31799200	Enhancers	A549	lung
13	chr12:31797200-31800400	Enhancers	Ovary	ovary
14	chr12:31797400-31799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:31797400-31800600	Enhancers	Primary B cells from cord blood	blood
16	chr12:31797600-31799800	Weak transcription	NHEK	skin
17	chr12:31797600-31803000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:31797800-31798000	Enhancers	Placenta	Placenta
19	chr12:31797800-31798200	Enhancers	HSMMtube	muscle
20	chr12:31797800-31798600	Enhancers	Primary hematopoietic stem cells	blood

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