Variant report

Variant	rs6503525
Chromosome Location	chr17:38095174-38095175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38094255..38096841-chr17:38137196..38138815,2	MCF-7	breast:
2	chr17:38082705..38085668-chr17:38094969..38098446,5	K562	blood:
3	chr17:38089487..38091759-chr17:38092539..38095742,3	K562	blood:
4	chr17:38083081..38090987-chr17:38092901..38098446,8	K562	blood:

Variant related genes	Relation type
ENSG00000264968	Chromatin interaction
ENSG00000172057	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12451084	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12451100	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12601749	0.91[ASN][1000 genomes]
rs12603481	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35123741	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3893044	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs3894194	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3902025	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4065985	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs4065986	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4795406	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4795408	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795409	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55739615	0.89[ASN][1000 genomes]
rs56199421	0.91[ASN][1000 genomes]
rs62068170	0.89[ASN][1000 genomes]
rs62068171	0.90[ASN][1000 genomes]
rs6503526	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216564	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8069202	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8079416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8080734	0.90[ASN][1000 genomes]
rs8081462	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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

Variant related diseases (count:1)

Disease	PMID	Source
Asthma	21150878	GWAS catalog

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6503525	GSDMA	cis	Nerve Tibial	GTEx
rs6503525	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs6503525	GSDMB	cis	parietal	SCAN
rs6503525	MED24	cis	parietal	SCAN
rs6503525	GSDMA	cis	Thyroid	GTEx
rs6503525	GSDMB	cis	lymphoblastoid	seeQTL
rs6503525	GSDMA	cis	Adipose Subcutaneous	GTEx
rs6503525	ORMDL3	cis	lymphoblastoid	seeQTL
rs6503525	MED24	cis	lymphoblastoid	GTEx
rs6503525	GSDMA	cis	Esophagus Muscularis	GTEx
rs6503525	MED24	cis	cerebellum	SCAN
rs6503525	GSDMA	cis	Artery Tibial	GTEx
rs6503525	SNORA21	cis	parietal	SCAN
rs6503525	GSDMB	cis	Whole Blood	GTEx
rs6503525	GSDMB	cis	cerebellum	SCAN
rs6503525	ORMDL3	cis	parietal	SCAN
rs6503525	GSDMA	cis	Artery Aorta	GTEx
rs6503525	GSDMA	cis	lung	GTEx
rs6503525	KRT222	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38085000-38095800	Weak transcription	Primary T cells from cord blood	blood
2	chr17:38085400-38095800	Weak transcription	Brain Substantia Nigra	brain
3	chr17:38085400-38096000	Weak transcription	Pancreas	Pancrea
4	chr17:38085600-38095600	Weak transcription	Fetal Intestine Small	intestine
5	chr17:38085800-38096000	Weak transcription	Brain Hippocampus Middle	brain
6	chr17:38086000-38095600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr17:38086200-38095600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:38086400-38095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:38086800-38095200	Weak transcription	NHLF	lung
10	chr17:38090400-38096000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:38090800-38095400	Weak transcription	A549	lung
12	chr17:38090800-38095600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38091600-38097800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:38092400-38095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38092600-38095200	Weak transcription	NH-A	brain
16	chr17:38092600-38095400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:38092600-38095400	Weak transcription	HSMMtube	muscle
18	chr17:38092600-38095600	Weak transcription	Left Ventricle	heart
19	chr17:38092600-38095600	Weak transcription	Stomach Mucosa	stomach
20	chr17:38092600-38096000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr17:38092800-38095200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:38092800-38095400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:38092800-38095400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr17:38092800-38095400	Weak transcription	HSMM	muscle
25	chr17:38092800-38095400	Weak transcription	Osteobl	bone
26	chr17:38093800-38095400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:38093800-38095600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:38093800-38096400	Enhancers	Primary B cells from cord blood	blood
29	chr17:38093800-38097000	Enhancers	GM12878-XiMat	blood
30	chr17:38094200-38095400	Weak transcription	Fetal Kidney	kidney
31	chr17:38094400-38095600	Enhancers	NHDF-Ad	bronchial
32	chr17:38094400-38097400	Enhancers	Fetal Thymus	thymus
33	chr17:38094600-38095600	Weak transcription	K562	blood
34	chr17:38094800-38096600	Enhancers	HepG2	liver
35	chr17:38094800-38100200	Weak transcription	Right Ventricle	heart
36	chr17:38095000-38095400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:38095000-38095600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:38095000-38096000	Weak transcription	Brain Inferior Temporal Lobe	brain

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