Variant report

Variant	rs3893044
Chromosome Location	chr17:38103016-38103017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38101089..38105078-chr17:38105781..38110100,7	K562	blood:
2	chr17:38098844..38100941-chr17:38101292..38104477,4	K562	blood:
3	chr17:38102879..38104734-chr17:38106799..38109127,2	MCF-7	breast:
4	chr17:38095595..38098522-chr17:38100216..38104569,3	K562	blood:

Variant related genes	Relation type
ENSG00000204913	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1007654	0.83[TSI][hapmap]
rs12451084	0.92[ASN][1000 genomes]
rs12451100	0.93[ASN][1000 genomes]
rs12601749	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12603481	0.83[ASN][1000 genomes]
rs35123741	0.83[ASN][1000 genomes]
rs3894194	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3902025	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4065985	0.88[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4065986	0.99[ASN][1000 genomes]
rs4795406	0.87[ASN][1000 genomes]
rs4795408	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4795409	0.82[ASN][1000 genomes]
rs55739615	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56199421	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62068170	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62068171	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503525	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs6503526	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7207600	0.94[YRI][hapmap]
rs7212938	0.86[JPT][hapmap]
rs7216564	0.89[ASN][1000 genomes]
rs7218742	0.94[YRI][hapmap]
rs7219080	0.81[TSI][hapmap]
rs8069202	0.86[ASN][1000 genomes]
rs8079416	0.81[CHD][hapmap];0.84[MEX][hapmap]
rs8080734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081462	0.89[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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3893044	MED24	cis	cerebellum	SCAN
rs3893044	MED24	cis	parietal	SCAN
rs3893044	GSDMA	cis	Esophagus Muscularis	GTEx
rs3893044	ORMDL3	cis	lymphoblastoid	seeQTL
rs3893044	GSDMA	cis	Thyroid	GTEx
rs3893044	GSDMA	cis	Artery Aorta	GTEx
rs3893044	GSDMA	cis	Artery Tibial	GTEx
rs3893044	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs3893044	PSMD3	cis	parietal	SCAN
rs3893044	CDC6	cis	cerebellum	SCAN
rs3893044	KRT222	cis	cerebellum	SCAN
rs3893044	PCGF2	cis	cerebellum	SCAN
rs3893044	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3893044	ORMDL3	cis	parietal	SCAN
rs3893044	GSDMB	cis	parietal	SCAN
rs3893044	GSDMA	cis	Nerve Tibial	GTEx
rs3893044	GSDMA	cis	lung	GTEx
rs3893044	GSDMB	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38096000-38104800	Weak transcription	Stomach Mucosa	stomach
2	chr17:38096400-38108400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:38097000-38104000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr17:38100000-38105800	Enhancers	Fetal Thymus	thymus
5	chr17:38100400-38104000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:38100600-38103800	Weak transcription	Primary B cells from cord blood	blood
7	chr17:38100800-38106800	Weak transcription	Spleen	Spleen
8	chr17:38100800-38107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr17:38100800-38108400	Weak transcription	Esophagus	oesophagus
10	chr17:38101000-38106200	Weak transcription	Liver	Liver
11	chr17:38101600-38104800	Weak transcription	Lung	lung
12	chr17:38102400-38103200	Weak transcription	Thymus	Thymus
13	chr17:38102400-38104400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:38102800-38103400	Enhancers	Placenta	Placenta
15	chr17:38102800-38103600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:38102800-38103600	Enhancers	HMEC	breast
17	chr17:38102800-38104000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:38102800-38104000	Enhancers	NHEK	skin
19	chr17:38102800-38104400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:38103000-38103200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:38103000-38103600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr17:38103000-38104600	Bivalent Enhancer	HepG2	liver

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