Variant report

Variant	rs3935280
Chromosome Location	chr17:38189055-38189056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38188992-38189777	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38188602..38190151-chr17:38209862..38212008,2	MCF-7	breast:
2	chr17:38186956..38189285-chr17:38277209..38280047,2	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
ENSG00000188895	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1042658	0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1045929	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs11078934	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871747	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12600856	0.86[EUR][1000 genomes]
rs12602172	0.86[EUR][1000 genomes]
rs12950335	0.92[ASN][1000 genomes]
rs2227315	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227322	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227336	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213762	0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826331	0.80[EUR][1000 genomes]
rs3884477	0.93[ASN][1000 genomes]
rs3936197	0.94[ASN][1000 genomes]
rs4794822	0.86[EUR][1000 genomes]
rs4794823	0.86[EUR][1000 genomes]
rs4794824	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795412	0.86[EUR][1000 genomes]
rs4795414	0.85[EUR][1000 genomes]
rs4795415	0.85[EUR][1000 genomes]
rs4795416	0.86[EUR][1000 genomes]
rs4795418	0.86[EUR][1000 genomes]
rs4795419	0.86[EUR][1000 genomes]
rs4795420	0.86[EUR][1000 genomes]
rs55771023	0.85[EUR][1000 genomes]
rs55846942	0.85[EUR][1000 genomes]
rs56922390	0.86[EUR][1000 genomes]
rs57065891	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57968500	0.86[EUR][1000 genomes]
rs59925331	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60082402	0.83[EUR][1000 genomes]
rs62065177	0.86[EUR][1000 genomes]
rs6503530	0.85[EUR][1000 genomes]
rs6503533	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7021	0.86[EUR][1000 genomes]
rs709591	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs709592	0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7208815	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7209755	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7214085	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221894	0.83[EUR][1000 genomes]
rs7502514	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7502912	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7503555	0.91[ASN][1000 genomes]
rs8065443	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8065519	0.83[EUR][1000 genomes]
rs8066846	0.91[ASN][1000 genomes]
rs8070454	0.86[EUR][1000 genomes]
rs8078692	0.92[ASN][1000 genomes]
rs8078723	0.83[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs8081692	0.85[EUR][1000 genomes]
rs868150	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9303283	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303284	0.94[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3935280	GSDMA	cis	Esophagus Muscularis	GTEx
rs3935280	GSDMA	cis	lung	GTEx
rs3935280	MED24	cis	Artery Tibial	GTEx
rs3935280	MED24	cis	cerebellum	SCAN
rs3935280	GSDMB	cis	cerebellum	SCAN
rs3935280	GSDMB	cis	Whole Blood	GTEx
rs3935280	PSMD3	cis	Frontal Cortex	GTEx
rs3935280	PCGF2	cis	cerebellum	SCAN
rs3935280	GSDMA	cis	Artery Aorta	GTEx
rs3935280	MED24	cis	Nerve Tibial	GTEx
rs3935280	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3935280	MED24	cis	Artery Aorta	GTEx
rs3935280	GSDMA	cis	Nerve Tibial	GTEx
rs3935280	MED24	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:38175000-38193800	Strong transcription	HepG2	liver
7	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
8	chr17:38175200-38193200	Strong transcription	Dnd41	blood
9	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
10	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
14	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
17	chr17:38176200-38193800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:38176400-38192400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:38177800-38191000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr17:38178200-38192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:38178600-38191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:38179000-38192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:38180400-38191200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:38180400-38192600	Strong transcription	Fetal Intestine Large	intestine
25	chr17:38180400-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:38181000-38192600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr17:38181400-38192600	Strong transcription	Fetal Lung	lung
28	chr17:38181400-38193200	Strong transcription	Brain Substantia Nigra	brain
29	chr17:38181400-38193400	Strong transcription	Brain Anterior Caudate	brain
30	chr17:38181800-38192600	Strong transcription	Osteobl	bone
31	chr17:38182800-38193800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:38183000-38195600	Strong transcription	Primary T cells from cord blood	blood
33	chr17:38183200-38193800	Strong transcription	Thymus	Thymus
34	chr17:38183400-38190800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:38183400-38191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:38183400-38192400	Strong transcription	Adipose Nuclei	Adipose
37	chr17:38183400-38192600	Strong transcription	NHLF	lung
38	chr17:38183400-38193200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:38183600-38189600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr17:38183600-38191400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr17:38183600-38191600	Strong transcription	A549	lung
42	chr17:38183600-38192200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:38183600-38192200	Strong transcription	Esophagus	oesophagus
44	chr17:38183600-38192600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr17:38183600-38192800	Strong transcription	Fetal Intestine Small	intestine
46	chr17:38183600-38193200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:38183600-38193400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:38183600-38193800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr17:38183800-38189200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr17:38183800-38191200	Strong transcription	Fetal Muscle Leg	muscle

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