Variant report

Variant	rs3744246
Chromosome Location	chr17:38084350-38084351
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	chr17:38082655-38084861	HepG2	liver:	n/a	n/a
2	CREB1	chr17:38082660-38084602	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:38083709-38084972	HepG2	liver:	n/a	n/a
4	CTCF	chr17:38084240-38084390	HMEC	breast:	n/a	n/a
5	HNF4A	chr17:38083633-38084444	HepG2	liver:	n/a	chr17:38084295-38084313 chr17:38084298-38084310
6	POLR2A	chr17:38083373-38084710	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr17:38084284-38084471	HepG2	liver:	n/a	n/a
8	POLR2A	chr17:38083419-38084357	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr17:38083607-38084521	HepG2	liver:	n/a	n/a
10	BHLHE40	chr17:38083665-38084468	HepG2	liver:	n/a	chr17:38083831-38083847 chr17:38084417-38084433 chr17:38083818-38083834
11	CTCF	chr17:38084220-38084370	HBMEC	blood vessel:	n/a	n/a
12	RAD21	chr17:38083550-38084467	H1-hESC	embryonic stem cell:	n/a	n/a
13	EP300	chr17:38083617-38084427	HepG2	liver:	n/a	chr17:38083832-38083848 chr17:38083881-38083897 chr17:38083780-38083789 chr17:38083888-38083897
14	POLR2A	chr17:38083011-38086107	IMR90	lung:	n/a	n/a
15	HEY1	chr17:38082704-38084446	HepG2	liver:	n/a	chr17:38083885-38083900
16	UBTF	chr17:38082997-38084492	K562	blood:	n/a	n/a
17	POLR2A	chr17:38083614-38085028	GM12891	blood:	n/a	n/a
18	POLR2A	chr17:38083622-38084575	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr17:38084235-38084478	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr17:38083581-38084397	A549	lung:	n/a	n/a
21	MYBL2	chr17:38083582-38084663	HepG2	liver:	n/a	n/a
22	POLR2A	chr17:38083565-38084539	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr17:38082638-38084726	HepG2	liver:	n/a	n/a
24	MTA3	chr17:38082426-38085085	GM12878	blood:	n/a	n/a
25	HMGN3	chr17:38083072-38084404	K562	blood:	n/a	n/a
26	POLR2A	chr17:38084324-38084728	GM12891	blood:	n/a	n/a
27	BHLHE40	chr17:38083702-38084526	K562	blood:	n/a	chr17:38083831-38083847 chr17:38084417-38084433 chr17:38083818-38083834
28	TEAD4	chr17:38083628-38084611	HepG2	liver:	n/a	n/a
29	EP300	chr17:38083687-38084412	HepG2	liver:	n/a	chr17:38083832-38083848 chr17:38083881-38083897 chr17:38083780-38083789 chr17:38083888-38083897
30	YY1	chr17:38082664-38084525	HepG2	liver:	n/a	chr17:38083355-38083366 chr17:38083650-38083664 chr17:38083773-38083787
31	MAX	chr17:38082999-38084779	A549	lung:	n/a	chr17:38083544-38083554 chr17:38083010-38083021
32	STAT5A	chr17:38083643-38084634	GM12878	blood:	n/a	n/a
33	CTCF	chr17:38084300-38084450	GM12871	blood:	n/a	n/a
34	POLR2A	chr17:38082689-38084594	GM19193	blood:	n/a	n/a
35	POLR2A	chr17:38082695-38085190	GM18505	blood:	n/a	n/a
36	TAF1	chr17:38082824-38084638	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIX5	chr17:38083452-38084720	A549	lung:	n/a	chr17:38083968-38083977 chr17:38083971-38083980 chr17:38083965-38083979 chr17:38083914-38083923 chr17:38083966-38083975 chr17:38083913-38083927 chr17:38083916-38083925
38	JUND	chr17:38083584-38084382	A549	lung:	n/a	n/a
39	POLR2A	chr17:38082598-38084553	HepG2	liver:	n/a	n/a
40	SP1	chr17:38083571-38084688	H1-hESC	embryonic stem cell:	n/a	chr17:38083687-38083701
41	PML	chr17:38083392-38084952	GM12878	blood:	n/a	n/a
42	MAZ	chr17:38082781-38084482	HepG2	liver:	n/a	chr17:38083544-38083554 chr17:38083010-38083021
43	POLR2A	chr17:38083557-38084542	HCT-116	colon:	n/a	n/a
44	ZNF143	chr17:38083639-38084388	H1-hESC	embryonic stem cell:	n/a	chr17:38083916-38083925 chr17:38083769-38083787 chr17:38083968-38083977 chr17:38083907-38083925 chr17:38083959-38083977 chr17:38083966-38083975 chr17:38083914-38083923 chr17:38083887-38083897
45	CEBPB	chr17:38083778-38084440	HepG2	liver:	n/a	n/a
46	NR2F2	chr17:38082735-38084415	K562	blood:	n/a	chr17:38083198-38083213
47	POLR2A	chr17:38082607-38084575	GM19099	blood:	n/a	n/a
48	ZEB1	chr17:38084167-38084523	GM12878	blood:	n/a	chr17:38084281-38084289
49	PBX3	chr17:38083579-38084510	A549	lung:	n/a	n/a
50	HCFC1	chr17:38082898-38085036	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38063849..38066832-chr17:38082215..38084527,2	MCF-7	breast:
2	chr17:38082350..38085117-chr17:38171214..38173786,2	K562	blood:
3	chr17:38082705..38085668-chr17:38094969..38098446,5	K562	blood:
4	chr17:38083081..38090987-chr17:38092901..38098446,8	K562	blood:
5	chr17:38082095..38085117-chr17:38171214..38173786,3	K562	blood:
6	chr17:37885255..37888241-chr17:38082917..38084897,2	K562	blood:

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

Variant related genes	Relation type
ORMDL3	TF binding region
ENSG00000204913	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000073605	Chromatin interaction
ENSG00000108342	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1008723	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1011082	0.86[ASN][1000 genomes]
rs1031458	0.86[ASN][1000 genomes]
rs1031460	0.86[ASN][1000 genomes]
rs10852936	0.88[JPT][hapmap]
rs11078925	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11078926	0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11078927	0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11078928	0.82[ASN][1000 genomes]
rs11557466	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11557467	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11650661	0.82[ASN][1000 genomes]
rs11651596	0.81[ASN][1000 genomes]
rs11655198	0.82[ASN][1000 genomes]
rs11655292	0.82[ASN][1000 genomes]
rs11870965	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12103884	0.82[ASN][1000 genomes]
rs12603332	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12709365	0.82[ASN][1000 genomes]
rs12936231	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12936409	0.81[ASN][1000 genomes]
rs12939832	0.81[ASN][1000 genomes]
rs12946393	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12949100	0.82[ASN][1000 genomes]
rs12950209	0.82[ASN][1000 genomes]
rs12950743	0.82[ASN][1000 genomes]
rs13380815	0.82[ASN][1000 genomes]
rs1453559	0.81[ASN][1000 genomes]
rs2290400	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2305479	0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2305480	0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2872516	0.83[ASN][1000 genomes]
rs34120102	0.82[ASN][1000 genomes]
rs36000226	0.82[ASN][1000 genomes]
rs3816470	0.88[JPT][hapmap]
rs4065275	0.91[ASN][1000 genomes]
rs4794820	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4795397	0.81[ASN][1000 genomes]
rs4795399	0.82[ASN][1000 genomes]
rs4795400	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4795401	0.86[ASN][1000 genomes]
rs4795402	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795403	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]
rs4795404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795405	0.89[CHD][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs56380902	0.86[ASN][1000 genomes]
rs62067034	0.82[ASN][1000 genomes]
rs6503524	0.86[ASN][1000 genomes]
rs7216389	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7216558	0.86[ASN][1000 genomes]
rs7219923	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7221605	0.83[ASN][1000 genomes]
rs7224129	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7224908	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7359623	0.82[ASN][1000 genomes]
rs8065777	0.86[ASN][1000 genomes]
rs8067378	0.82[ASN][1000 genomes]
rs8069176	0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs8074437	0.84[ASN][1000 genomes]
rs8076131	0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs869402	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs883770	0.82[ASN][1000 genomes]
rs921649	0.86[ASN][1000 genomes]
rs921650	0.86[ASN][1000 genomes]
rs9303279	0.85[ASN][1000 genomes]
rs9303280	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9303281	0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3744246	KRTAP4-5	cis	cerebellum	SCAN
rs3744246	ORMDL3	cis	lymphoblastoid	seeQTL
rs3744246	ORMDL3	cis	parietal	SCAN
rs3744246	GSDMB	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38082400-38084400	Active TSS	Rectal Smooth Muscle	rectum
2	chr17:38082600-38084400	Active TSS	Liver	Liver
3	chr17:38082600-38084800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr17:38082800-38084400	Active TSS	Fetal Kidney	kidney
5	chr17:38082800-38084400	Active TSS	GM12878-XiMat	blood
6	chr17:38082800-38084600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr17:38082800-38084600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr17:38082800-38084600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr17:38082800-38084600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr17:38082800-38084800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr17:38082800-38084800	Bivalent/Poised TSS	HepG2	liver
12	chr17:38083000-38084400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr17:38083000-38084400	Active TSS	Small Intestine	intestine
14	chr17:38083000-38084600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:38083000-38084600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:38083000-38084600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr17:38083000-38084600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr17:38083000-38084600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr17:38083000-38084600	Active TSS	Gastric	stomach
20	chr17:38083000-38084800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr17:38083000-38084800	Active TSS	Ovary	ovary
22	chr17:38083000-38085000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:38083000-38085000	Active TSS	Aorta	Aorta
24	chr17:38083200-38084400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr17:38083200-38084400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr17:38083200-38084400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr17:38083200-38084400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr17:38083200-38084400	Active TSS	Colon Smooth Muscle	Colon
29	chr17:38083200-38084400	Active TSS	Fetal Heart	heart
30	chr17:38083200-38084400	Active TSS	Psoas Muscle	Psoas
31	chr17:38083200-38084400	Active TSS	Stomach Mucosa	stomach
32	chr17:38083200-38084400	Active TSS	Dnd41	blood
33	chr17:38083200-38084400	Active TSS	K562	blood
34	chr17:38083200-38084600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:38083200-38084600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:38083200-38084600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:38083200-38084600	Active TSS	Brain Angular Gyrus	brain
38	chr17:38083200-38084600	Active TSS	Brain Anterior Caudate	brain
39	chr17:38083200-38084600	Active TSS	Brain Substantia Nigra	brain
40	chr17:38083200-38084600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr17:38083200-38084600	Active TSS	Fetal Stomach	stomach
42	chr17:38083200-38084600	Active TSS	Right Atrium	heart
43	chr17:38083200-38084800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:38083200-38084800	Active TSS	Fetal Brain Female	brain
45	chr17:38083200-38084800	Active TSS	Lung	lung
46	chr17:38083400-38084400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:38083400-38084400	Active TSS	Brain Cingulate Gyrus	brain
48	chr17:38083400-38084400	Active TSS	Brain Germinal Matrix	brain
49	chr17:38083400-38084400	Active TSS	Brain Hippocampus Middle	brain
50	chr17:38083400-38084400	Active TSS	Duodenum Mucosa	Duodenum

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