Variant report

Variant	rs12941811
Chromosome Location	chr17:38159335-38159336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38152599..38155402-chr17:38158806..38161805,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1042658	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1045929	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11658328	0.82[EUR][1000 genomes]
rs11871747	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12453764	0.82[EUR][1000 genomes]
rs12600856	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602172	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940405	0.81[EUR][1000 genomes]
rs2227315	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2227322	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2227336	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2241244	0.82[EUR][1000 genomes]
rs2241245	0.82[EUR][1000 genomes]
rs3213762	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3816472	0.81[EUR][1000 genomes]
rs3826331	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3859187	0.82[EUR][1000 genomes]
rs4065321	0.82[EUR][1000 genomes]
rs4433838	0.82[EUR][1000 genomes]
rs4794822	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794823	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794824	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4795412	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795414	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795415	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795416	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795418	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795419	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795420	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55771023	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55846942	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56922390	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57065891	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57968500	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59925331	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60082402	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62065177	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6503530	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7021	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709591	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs709592	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7208815	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7209755	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7214085	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7221894	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7222039	0.96[ASN][1000 genomes]
rs8065519	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066582	0.82[EUR][1000 genomes]
rs8067817	0.96[ASN][1000 genomes]
rs8068260	0.90[ASN][1000 genomes]
rs8070444	0.82[EUR][1000 genomes]
rs8070454	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8071037	0.82[EUR][1000 genomes]
rs8072548	0.96[ASN][1000 genomes]
rs8073254	0.82[EUR][1000 genomes]
rs8078723	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081692	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9915252	0.82[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	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
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12941811	GSDMA	cis	Nerve Tibial	GTEx
rs12941811	MED24	cis	Thyroid	GTEx
rs12941811	MED24	cis	Nerve Tibial	GTEx
rs12941811	GSDMA	cis	lung	GTEx
rs12941811	GSDMA	cis	Esophagus Muscularis	GTEx
rs12941811	GSDMA	cis	Adipose Subcutaneous	GTEx
rs12941811	MED24	cis	Artery Tibial	GTEx
rs12941811	MED24	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38152200-38160600	Weak transcription	Psoas Muscle	Psoas
2	chr17:38152200-38160800	Weak transcription	K562	blood
3	chr17:38153200-38166400	Weak transcription	Fetal Lung	lung
4	chr17:38153400-38166200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:38153400-38166600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:38153600-38160400	Weak transcription	HSMMtube	muscle
7	chr17:38153600-38160600	Weak transcription	Stomach Mucosa	stomach
8	chr17:38153800-38160600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:38153800-38166200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:38153800-38166200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:38154200-38161000	Weak transcription	Lung	lung
13	chr17:38154200-38166400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr17:38154400-38160400	Weak transcription	HepG2	liver
15	chr17:38154400-38166200	Weak transcription	Dnd41	blood
16	chr17:38154400-38166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:38154600-38160800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:38154600-38166200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr17:38154600-38166400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:38154600-38170000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:38154600-38170200	Weak transcription	Esophagus	oesophagus
22	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
23	chr17:38155000-38160600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:38155000-38160600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr17:38155000-38166200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:38155000-38166400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr17:38155000-38170000	Weak transcription	HSMM	muscle
28	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
30	chr17:38155400-38170200	Weak transcription	Placenta	Placenta
31	chr17:38155600-38164200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr17:38155600-38166600	Weak transcription	Fetal Thymus	thymus
33	chr17:38155600-38169600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr17:38155600-38169800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:38155800-38160400	Weak transcription	Fetal Muscle Leg	muscle
36	chr17:38155800-38161000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:38155800-38171800	Weak transcription	Spleen	Spleen

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