Variant report

Variant	rs4795403
Chromosome Location	chr17:38085722-38085723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr17:38085577-38085755	GM12878	blood:	n/a	n/a
2	SMC3	chr17:38085637-38085755	GM12878	blood:	n/a	n/a
3	GATA3	chr17:38085257-38086495	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr17:38085074-38086516	SK-N-SH	brain:	n/a	n/a
5	CEBPB	chr17:38085441-38086369	A549	lung:	n/a	n/a
6	EP300	chr17:38085528-38085746	GM12878	blood:	n/a	n/a
7	FOS	chr17:38085342-38086444	MCF10A-Er-Src	breast:	n/a	n/a
8	JUN	chr17:38085365-38085870	K562	blood:	n/a	n/a
9	RUNX3	chr17:38085408-38085936	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:38083011-38086107	IMR90	lung:	n/a	n/a
11	NFIC	chr17:38085166-38086181	GM12878	blood:	n/a	n/a
12	STAT3	chr17:38085356-38086394	MCF10A-Er-Src	breast:	n/a	n/a
13	PBX3	chr17:38085685-38085904	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr17:38085441-38085838	K562	blood:	n/a	n/a
15	IKZF1	chr17:38085309-38086105	GM12878	blood:	n/a	n/a
16	BRCA1	chr17:38085439-38086014	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr17:38085342-38086387	MCF10A-Er-Src	breast:	n/a	n/a
18	JUN	chr17:38084822-38086414	K562	blood:	n/a	chr17:38086149-38086162 chr17:38084931-38084940
19	FOS	chr17:38085375-38086415	MCF10A-Er-Src	breast:	n/a	n/a
20	ESR1	chr17:38085498-38085969	T-47D	breast:	n/a	n/a
21	TBL1XR1	chr17:38085606-38085786	GM12878	blood:	n/a	n/a
22	MTA3	chr17:38085306-38086158	GM12878	blood:	n/a	n/a
23	ATF1	chr17:38085338-38085868	K562	blood:	n/a	n/a
24	BCL11A	chr17:38085439-38085809	GM12878	blood:	n/a	n/a
25	SP1	chr17:38085285-38086444	A549	lung:	n/a	n/a
26	NFIC	chr17:38085292-38086445	SK-N-SH	brain:	n/a	n/a
27	RUNX3	chr17:38085146-38086078	GM12878	blood:	n/a	n/a
28	EP300	chr17:38085457-38086348	Hela-S3	cervix:	n/a	n/a
29	MEF2C	chr17:38085355-38085983	GM12878	blood:	n/a	n/a
30	STAT3	chr17:38085311-38086313	Hela-S3	cervix:	n/a	n/a
31	JUN	chr17:38085398-38085880	K562	blood:	n/a	n/a
32	ESR1	chr17:38085411-38086341	T-47D	breast:	n/a	n/a
33	MEF2A	chr17:38085139-38086049	SK-N-SH	brain:	n/a	n/a
34	EP300	chr17:38085198-38086442	SK-N-SH	brain:	n/a	n/a
35	BATF	chr17:38085449-38085820	GM12878	blood:	n/a	n/a
36	GATA2	chr17:38085302-38085911	HUVEC	blood vessel:	n/a	n/a
37	PRDM1	chr17:38085457-38086231	Hela-S3	cervix:	n/a	n/a
38	GATA3	chr17:38085502-38086466	T-47D	breast:	n/a	n/a
39	MYC	chr17:38085418-38086171	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr17:38085260-38086175	HUVEC	blood vessel:	n/a	n/a
41	PBX3	chr17:38085249-38086317	SK-N-SH	brain:	n/a	n/a
42	BATF	chr17:38085369-38085841	GM12878	blood:	n/a	n/a
43	RCOR1	chr17:38085550-38085855	K562	blood:	n/a	n/a
44	FOXA1	chr17:38085611-38086442	T-47D	breast:	n/a	n/a
45	MAFK	chr17:38085295-38085754	Hela-S3	cervix:	n/a	n/a
46	FOSL2	chr17:38085392-38085870	SK-N-SH	brain:	n/a	n/a
47	FOXM1	chr17:38085274-38085992	GM12878	blood:	n/a	n/a
48	CREB1	chr17:38085236-38086030	GM12878	blood:	n/a	n/a
49	RCOR1	chr17:38085515-38086387	Hela-S3	cervix:	n/a	n/a
50	RXRA	chr17:38085216-38085947	SK-N-SH	brain:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38083081..38090987-chr17:38092901..38098446,8	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC3C-1	chr17:38084198-38086404	NONHSAT053500

No data

Variant related genes	Relation type
ORMDL3	TF binding region
ENSG00000204913	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1008723	0.80[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1011082	0.85[ASN][1000 genomes]
rs1031458	0.85[ASN][1000 genomes]
rs1031460	0.85[ASN][1000 genomes]
rs10852936	0.88[JPT][hapmap]
rs11078925	0.88[JPT][hapmap]
rs11078926	0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11078927	0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11078928	0.81[ASN][1000 genomes]
rs11557466	0.82[JPT][hapmap]
rs11557467	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11650661	0.81[ASN][1000 genomes]
rs11651596	0.81[ASN][1000 genomes]
rs11655198	0.81[ASN][1000 genomes]
rs11655292	0.81[ASN][1000 genomes]
rs11870965	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12103884	0.81[ASN][1000 genomes]
rs12603332	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12709365	0.81[ASN][1000 genomes]
rs12936231	0.80[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12936409	0.81[ASN][1000 genomes]
rs12939832	0.81[ASN][1000 genomes]
rs12946393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949100	0.81[ASN][1000 genomes]
rs12950209	0.81[ASN][1000 genomes]
rs12950743	0.81[ASN][1000 genomes]
rs13380815	0.81[ASN][1000 genomes]
rs2290400	0.80[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2305479	0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2305480	0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2872516	0.82[ASN][1000 genomes]
rs34120102	0.81[ASN][1000 genomes]
rs36000226	0.81[ASN][1000 genomes]
rs3744246	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816470	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs4065275	0.90[ASN][1000 genomes]
rs4794820	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4795399	0.81[ASN][1000 genomes]
rs4795400	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4795401	0.85[ASN][1000 genomes]
rs4795402	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795405	0.89[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs56380902	0.85[ASN][1000 genomes]
rs62067034	0.81[ASN][1000 genomes]
rs6503524	0.85[ASN][1000 genomes]
rs7216389	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7216558	0.85[ASN][1000 genomes]
rs7219923	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7221605	0.82[ASN][1000 genomes]
rs7224129	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7224908	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359623	0.81[ASN][1000 genomes]
rs8065777	0.85[ASN][1000 genomes]
rs8067378	0.81[ASN][1000 genomes]
rs8069176	0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs8074437	0.83[ASN][1000 genomes]
rs8076131	0.89[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs869402	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs883770	0.81[ASN][1000 genomes]
rs907092	0.80[CHD][hapmap]
rs921649	0.85[ASN][1000 genomes]
rs921650	0.85[ASN][1000 genomes]
rs9303279	0.85[ASN][1000 genomes]
rs9303280	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs9303281	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4795403	PARD3	trans	lymphoblastoid	seeQTL
rs4795403	ORMDL3	cis	parietal	SCAN
rs4795403	ORMDL3	cis	multi-tissue	Pritchard
rs4795403	ORMDL3	cis	lymphoblastoid	seeQTL
rs4795403	KRTAP4-5	cis	cerebellum	SCAN
rs4795403	GSDMB	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38084000-38086200	Flanking Active TSS	NH-A	brain
2	chr17:38084000-38086200	Flanking Active TSS	Osteobl	bone
3	chr17:38084000-38086400	Flanking Active TSS	HUVEC	blood vessel
4	chr17:38084200-38086000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr17:38084200-38086200	Flanking Active TSS	A549	lung
6	chr17:38084400-38086000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr17:38084400-38086200	Flanking Active TSS	Fetal Heart	heart
8	chr17:38084400-38086200	Flanking Active TSS	GM12878-XiMat	blood
9	chr17:38084400-38086400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:38084600-38085800	Enhancers	Fetal Thymus	thymus
11	chr17:38084600-38085800	Enhancers	NHEK	skin
12	chr17:38084600-38086000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38084600-38086000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr17:38084600-38086000	Enhancers	Placenta	Placenta
15	chr17:38084600-38086000	Enhancers	Small Intestine	intestine
16	chr17:38084600-38086400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38084600-38086400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr17:38084800-38085800	Enhancers	NHDF-Ad	bronchial
19	chr17:38084800-38086000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:38084800-38086200	Enhancers	HSMMtube	muscle
21	chr17:38084800-38086400	Enhancers	HMEC	breast
22	chr17:38084800-38086600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:38085000-38085800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:38085000-38085800	Enhancers	Fetal Kidney	kidney
25	chr17:38085000-38085800	Enhancers	Fetal Lung	lung
26	chr17:38085000-38086000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:38085000-38086000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:38085000-38086000	Enhancers	Brain Angular Gyrus	brain
29	chr17:38085000-38086000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:38085000-38086000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr17:38085000-38086000	Flanking Active TSS	Hela-S3	cervix
32	chr17:38085000-38086200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr17:38085000-38086400	Enhancers	K562	blood
34	chr17:38085000-38086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:38085000-38089400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr17:38085000-38089600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:38085000-38090000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:38085000-38090000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:38085000-38090000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:38085000-38090200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:38085000-38090200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr17:38085000-38095800	Weak transcription	Primary T cells from cord blood	blood
43	chr17:38085200-38085800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:38085200-38085800	Enhancers	Brain Hippocampus Middle	brain
45	chr17:38085200-38086000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:38085200-38086000	Enhancers	Adipose Nuclei	Adipose
47	chr17:38085200-38086000	Enhancers	Liver	Liver
48	chr17:38085200-38086000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
49	chr17:38085200-38086000	Enhancers	Stomach Smooth Muscle	stomach
50	chr17:38085200-38086000	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links