Variant report

Variant	rs868150
Chromosome Location	chr17:38213359-38213360
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	chr17:38211636..38214646-chr17:38294140..38297702,3	K562	blood:

Variant related genes	Relation type
ENSG00000108349	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1042658	0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1045929	0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11078934	0.86[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs11871747	0.84[ASN][1000 genomes]
rs12950335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227315	0.86[ASN][1000 genomes]
rs2227322	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2227336	0.86[ASN][1000 genomes]
rs3213762	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[ASN][1000 genomes]
rs3884477	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935280	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3936197	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4794824	0.86[ASN][1000 genomes]
rs57065891	0.86[ASN][1000 genomes]
rs59925331	0.86[ASN][1000 genomes]
rs62065216	0.81[EUR][1000 genomes]
rs709591	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs709592	0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7208815	0.84[ASN][1000 genomes]
rs7209755	0.86[ASN][1000 genomes]
rs7214085	0.86[ASN][1000 genomes]
rs7502514	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs7502912	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7503555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8065443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066846	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8078692	0.99[ASN][1000 genomes]
rs8078723	0.83[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs9303283	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9303284	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs868150	GSDMA	cis	lung	GTEx
rs868150	PCGF2	cis	cerebellum	SCAN
rs868150	GSDMA	cis	Adipose Subcutaneous	GTEx
rs868150	CCL2	cis	cerebellum	SCAN
rs868150	PSMD3	cis	parietal	SCAN
rs868150	MED24	cis	Artery Tibial	GTEx
rs868150	MED24	cis	cerebellum	SCAN
rs868150	MED24	cis	Nerve Tibial	GTEx
rs868150	KRT222	cis	cerebellum	SCAN
rs868150	GSDMB	cis	cerebellum	SCAN
rs868150	MED24	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38211000-38217400	Weak transcription	Gastric	stomach
2	chr17:38211200-38213800	Weak transcription	Right Ventricle	heart
3	chr17:38211200-38214000	Weak transcription	Spleen	Spleen
4	chr17:38211200-38214200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:38211200-38214400	Weak transcription	Fetal Thymus	thymus
6	chr17:38211200-38215000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr17:38211200-38217200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:38211200-38217200	Weak transcription	Esophagus	oesophagus
9	chr17:38211200-38217200	Weak transcription	Pancreas	Pancrea
10	chr17:38211200-38217600	Weak transcription	Colonic Mucosa	Colon
11	chr17:38211200-38218600	Weak transcription	Left Ventricle	heart
12	chr17:38211200-38218600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:38211400-38213800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:38211400-38214000	Weak transcription	Adipose Nuclei	Adipose
15	chr17:38211400-38214000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr17:38211400-38214200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:38211400-38214200	Weak transcription	Liver	Liver
18	chr17:38211400-38214200	Weak transcription	Colon Smooth Muscle	Colon
19	chr17:38211400-38214200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr17:38211400-38214200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr17:38211400-38214200	Weak transcription	Osteobl	bone
22	chr17:38211400-38214400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:38211400-38214400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:38211400-38214400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:38211400-38214400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:38211400-38214400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr17:38211400-38214400	Weak transcription	Fetal Lung	lung
28	chr17:38211400-38214400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:38211400-38214400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:38211400-38214400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr17:38211400-38214400	Weak transcription	Stomach Mucosa	stomach
32	chr17:38211400-38214400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr17:38211400-38214400	Weak transcription	Dnd41	blood
34	chr17:38211400-38214400	Weak transcription	HUVEC	blood vessel
35	chr17:38211400-38214600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr17:38211400-38215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:38211400-38216000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:38211400-38216200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:38211400-38217400	Weak transcription	Brain Anterior Caudate	brain
40	chr17:38211400-38217600	Weak transcription	Fetal Intestine Large	intestine
41	chr17:38211400-38218000	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:38211400-38218200	Weak transcription	Primary T cells from cord blood	blood
43	chr17:38211400-38218200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:38211400-38218200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr17:38211400-38218200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:38211400-38218200	Weak transcription	Hela-S3	cervix
47	chr17:38211400-38218400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr17:38211400-38218400	Weak transcription	Brain Substantia Nigra	brain
49	chr17:38211400-38218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr17:38211600-38214200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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