Variant report

Variant	rs55773960
Chromosome Location	chr6:79945942-79945943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:79945558-79945951	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79787878..79790499-chr6:79943656..79946271,3	K562	blood:
3	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK1BP1-1	chr6:79943779-79946510	ENSG00000247783
2	lnc-IRAK1BP1-1	chr6:79943779-79946517	NONHSAT113679
3	lnc-IRAK1BP1-1	chr6:79944457-79946310	NONHSAT113680
4	lnc-IRAK1BP1-1	chr6:79943779-79946514	ENSG00000270362.1

No data

Variant related genes	Relation type
HMGN3	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13200164	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203405	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203510	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13209338	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13209772	0.98[EUR][1000 genomes]
rs13210296	0.98[EUR][1000 genomes]
rs13210935	0.98[EUR][1000 genomes]
rs13212378	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13213305	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217071	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217706	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220697	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360569	0.98[EUR][1000 genomes]
rs34057607	0.96[EUR][1000 genomes]
rs34493475	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34688736	0.94[EUR][1000 genomes]
rs35034704	0.89[AFR][1000 genomes]
rs35099838	0.92[EUR][1000 genomes]
rs35201024	0.98[EUR][1000 genomes]
rs35233121	0.98[EUR][1000 genomes]
rs35237040	0.94[EUR][1000 genomes]
rs35332837	0.98[EUR][1000 genomes]
rs35742788	0.98[EUR][1000 genomes]
rs35838792	0.89[EUR][1000 genomes]
rs36116051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66513375	0.98[EUR][1000 genomes]
rs66633427	0.98[EUR][1000 genomes]
rs66809524	0.98[EUR][1000 genomes]
rs66869917	0.98[EUR][1000 genomes]
rs72893783	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9448670	0.92[EUR][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55773960	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79944400-79948400	Weak transcription	Left Ventricle	heart
2	chr6:79944400-79948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:79944400-79948600	Weak transcription	Stomach Mucosa	stomach
4	chr6:79944400-79948800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:79944400-79950400	Weak transcription	Lung	lung
6	chr6:79944600-79948600	Weak transcription	Ovary	ovary
7	chr6:79944600-79948600	Weak transcription	Pancreas	Pancrea
8	chr6:79944600-79948600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:79944800-79946200	Weak transcription	Thymus	Thymus
10	chr6:79944800-79946200	Weak transcription	NHDF-Ad	bronchial
11	chr6:79944800-79947400	Weak transcription	NH-A	brain
12	chr6:79944800-79947600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:79944800-79947600	Weak transcription	GM12878-XiMat	blood
14	chr6:79944800-79948600	Weak transcription	Liver	Liver
15	chr6:79944800-79948600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:79944800-79948600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:79944800-79948600	Weak transcription	Right Atrium	heart
18	chr6:79944800-79948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:79944800-79948600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:79944800-79948600	Weak transcription	NHEK	skin
21	chr6:79944800-79948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:79944800-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:79944800-79948800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:79944800-79949200	Weak transcription	HMEC	breast
25	chr6:79944800-79950400	Weak transcription	Right Ventricle	heart
26	chr6:79945000-79946200	Weak transcription	Fetal Thymus	thymus
27	chr6:79945000-79947800	Weak transcription	Hela-S3	cervix
28	chr6:79945000-79948400	Weak transcription	Fetal Heart	heart
29	chr6:79945000-79948400	Weak transcription	HepG2	liver
30	chr6:79945000-79948600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr6:79945000-79948600	Weak transcription	Placenta	Placenta
32	chr6:79945000-79948800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:79945000-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:79945000-79949000	Weak transcription	Psoas Muscle	Psoas
35	chr6:79945000-79955400	Weak transcription	Aorta	Aorta

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