Variant report

Variant	rs9303279
Chromosome Location	chr17:38073968-38073969
allele	C/G
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	chr17:38073964-38073973	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38073834..38076577-chr17:38077829..38081795,4	MCF-7	breast:
2	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
3	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:

Variant related genes	Relation type
GSDMB	TF binding region
ENSG00000172057	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1008723	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1011082	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031458	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1031460	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11078925	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11078926	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078927	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078928	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11557466	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11557467	0.94[ASN][1000 genomes]
rs11650661	0.95[ASN][1000 genomes]
rs11651596	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11655198	0.95[ASN][1000 genomes]
rs11655292	0.95[ASN][1000 genomes]
rs11870965	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12103884	0.95[ASN][1000 genomes]
rs12453507	0.89[ASN][1000 genomes]
rs12603332	0.95[ASN][1000 genomes]
rs12709365	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12936231	0.95[ASN][1000 genomes]
rs12936409	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12939832	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12946393	0.85[ASN][1000 genomes]
rs12949100	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12950209	0.95[ASN][1000 genomes]
rs12950743	0.95[ASN][1000 genomes]
rs13380815	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1453559	0.94[ASN][1000 genomes]
rs2290400	0.97[ASN][1000 genomes]
rs2305479	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2305480	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2872516	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34120102	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs36000226	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3744246	0.85[ASN][1000 genomes]
rs4065275	0.95[ASN][1000 genomes]
rs4794820	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4795397	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4795399	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795400	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795401	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4795402	0.85[ASN][1000 genomes]
rs4795403	0.85[ASN][1000 genomes]
rs4795404	0.85[ASN][1000 genomes]
rs4795405	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56380902	0.99[ASN][1000 genomes]
rs62067034	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6503524	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213668	0.83[ASN][1000 genomes]
rs7216389	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7216558	0.99[ASN][1000 genomes]
rs7219923	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221605	0.96[ASN][1000 genomes]
rs7221814	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7224129	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224908	0.85[ASN][1000 genomes]
rs7359623	0.95[ASN][1000 genomes]
rs8065777	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8067378	0.95[ASN][1000 genomes]
rs8069176	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074437	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8076131	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869402	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883770	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs921649	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921650	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303280	0.99[ASN][1000 genomes]
rs9303281	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9906951	0.93[ASN][1000 genomes]
rs9916765	0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9303279	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs9303279	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs9303279	IKZF3	cis	multi-tissue	Pritchard
rs9303279	ORMDL3	cis	multi-tissue	Pritchard
rs9303279	ORMDL3	cis	Whole Blood	GTEx
rs9303279	GSDMB	cis	Whole Blood	GTEx
rs9303279	PGAP3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38049200-38075400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:38052600-38074200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:38055600-38077400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38056800-38074600	Weak transcription	NH-A	brain
5	chr17:38057200-38074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:38057400-38075400	Weak transcription	HSMM	muscle
7	chr17:38057600-38076600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:38057800-38077600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:38058000-38074600	Weak transcription	Left Ventricle	heart
10	chr17:38058200-38076200	Weak transcription	Fetal Lung	lung
11	chr17:38058200-38077800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:38058400-38075400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:38058600-38075400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:38058600-38077400	Weak transcription	Colon Smooth Muscle	Colon
15	chr17:38059000-38082400	Weak transcription	Psoas Muscle	Psoas
16	chr17:38059200-38075400	Weak transcription	Brain Hippocampus Middle	brain
17	chr17:38059400-38074000	Weak transcription	Small Intestine	intestine
18	chr17:38059800-38077200	Weak transcription	Esophagus	oesophagus
19	chr17:38060000-38077400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr17:38060400-38081600	Weak transcription	Fetal Brain Male	brain
21	chr17:38060800-38075600	Strong transcription	Primary T cells from cord blood	blood
22	chr17:38061000-38074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:38061200-38074000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:38061400-38075400	Weak transcription	Right Ventricle	heart
25	chr17:38061600-38074200	Strong transcription	Fetal Thymus	thymus
26	chr17:38061800-38081000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:38062200-38075200	Weak transcription	Spleen	Spleen
28	chr17:38062200-38075400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:38062400-38075400	Weak transcription	Dnd41	blood
30	chr17:38062800-38078200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:38063600-38077000	Weak transcription	Pancreas	Pancrea
32	chr17:38063800-38074200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:38063800-38075400	Weak transcription	NHEK	skin
34	chr17:38064000-38075200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr17:38065600-38075400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:38065800-38075400	Weak transcription	NHLF	lung
37	chr17:38066000-38074200	Weak transcription	Fetal Brain Female	brain
38	chr17:38066400-38074600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr17:38066600-38075400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:38066600-38078000	Weak transcription	Fetal Heart	heart
41	chr17:38066800-38074200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr17:38066800-38076200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr17:38066800-38076600	Weak transcription	HSMMtube	muscle
44	chr17:38067000-38074400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr17:38067000-38075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:38067000-38075400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr17:38067000-38075400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:38067000-38075400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr17:38067800-38074200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:38067800-38075000	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links