Variant report

Variant	rs55906604
Chromosome Location	chr17:34077954-34077955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:34056822..34061069-chr17:34076136..34079355,3	K562	blood:
2	chr17:34075379..34078199-chr17:34134410..34136040,2	K562	blood:
3	chr17:34076253..34080125-chr17:34136044..34138014,4	K562	blood:
4	chr17:34077398..34079510-chr17:34136909..34138877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267578	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000141150	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2242596	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2242597	0.89[EUR][1000 genomes]
rs2280786	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2280788	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2293789	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28914802	0.89[EUR][1000 genomes]
rs28914816	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28914817	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28914819	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3826454	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4251700	0.89[EUR][1000 genomes]
rs4251739	0.89[EUR][1000 genomes]
rs55680144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781042	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55792948	1.00[EUR][1000 genomes]
rs55799023	0.89[EUR][1000 genomes]
rs55833673	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55846484	0.89[EUR][1000 genomes]
rs55915639	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55951822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56029903	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56077005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56111312	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56135703	1.00[AFR][1000 genomes]
rs56170514	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56181735	0.89[EUR][1000 genomes]
rs56221144	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56262662	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56305516	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56347933	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56382694	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72483217	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9896368	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55906604	GAS2L2	cis	Heart Left Ventricle	GTEx
rs55906604	GAS2L2	cis	Muscle Skeletal	GTEx
rs55906604	GAS2L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34071000-34079800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:34074200-34078200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr17:34074600-34078400	Enhancers	HMEC	breast
4	chr17:34074800-34078400	Enhancers	NHEK	skin
5	chr17:34075600-34078200	Bivalent Enhancer	Adipose Nuclei	Adipose
6	chr17:34076600-34078000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:34076800-34078000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
8	chr17:34077200-34079400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:34077400-34078200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:34077400-34078800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:34077400-34079400	Weak transcription	Pancreas	Pancrea
12	chr17:34077600-34078000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr17:34077600-34078000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:34077600-34078200	Enhancers	Hela-S3	cervix
15	chr17:34077600-34078400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:34077600-34078400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:34077600-34079400	Weak transcription	Right Atrium	heart
18	chr17:34077800-34078000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr17:34077800-34078000	Bivalent Enhancer	Osteobl	bone
20	chr17:34077800-34078200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:34077800-34078200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:34077800-34078200	Bivalent Enhancer	HepG2	liver
23	chr17:34077800-34078400	Enhancers	Esophagus	oesophagus
24	chr17:34077800-34078400	Enhancers	K562	blood
25	chr17:34077800-34079200	Weak transcription	A549	lung
26	chr17:34077800-34079400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr17:34077800-34079800	Weak transcription	Right Ventricle	heart

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