Variant report

Variant	rs5742926
Chromosome Location	chr2:190648805-190648806
allele	G/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	chr2:190648087-190649835	GM18505	blood:	n/a	n/a
2	POLR2A	chr2:190648353-190649755	GM12891	blood:	n/a	n/a
3	MYBL2	chr2:190648052-190650090	HepG2	liver:	n/a	n/a
4	STAT1	chr2:190648400-190649595	GM12878	blood:	n/a	chr2:190649472-190649495
5	MAX	chr2:190648341-190649658	H1-hESC	embryonic stem cell:	n/a	chr2:190649600-190649609
6	ELF1	chr2:190648402-190649534	GM12878	blood:	n/a	n/a
7	E2F6	chr2:190648696-190649648	K562	blood:	n/a	chr2:190649437-190649448 chr2:190649436-190649448
8	CTCF	chr2:190648660-190648810	GM12866	blood:	n/a	n/a
9	BRCA1	chr2:190648444-190649610	HepG2	liver:	n/a	n/a
10	MYC	chr2:190648093-190649751	K562	blood:	n/a	chr2:190649600-190649609
11	MYC	chr2:190648303-190649722	K562	blood:	n/a	chr2:190649600-190649609
12	NFYA	chr2:190648692-190649328	K562	blood:	n/a	chr2:190649114-190649132
13	BRCA1	chr2:190648802-190649664	Hela-S3	cervix:	n/a	n/a
14	E2F6	chr2:190648560-190649795	H1-hESC	embryonic stem cell:	n/a	chr2:190649437-190649448 chr2:190649436-190649448
15	GABPA	chr2:190647878-190649564	A549	lung:	n/a	chr2:190649206-190649217
16	HA-E2F1	chr2:190648527-190649636	Hela-S3	cervix:	n/a	chr2:190649198-190649209 chr2:190649436-190649448
17	POLR2A	chr2:190648524-190649546	A549	lung:	n/a	n/a
18	PML	chr2:190648447-190649698	GM12878	blood:	n/a	n/a
19	REST	chr2:190648729-190649060	GM12878	blood:	n/a	chr2:190648965-190648972
20	POLR2A	chr2:190647979-190649869	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr2:190648434-190649600	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:190648112-190650548	H1-hESC	embryonic stem cell:	n/a	n/a
23	EP300	chr2:190648311-190649448	HepG2	liver:	n/a	n/a
24	EBF1	chr2:190648462-190649301	GM12878	blood:	n/a	n/a
25	REST	chr2:190648516-190649530	SK-N-SH	brain:	n/a	chr2:190648965-190648972
26	GABPA	chr2:190647952-190649551	SK-N-SH	brain:	n/a	chr2:190649206-190649217
27	TBP	chr2:190648693-190649911	Hela-S3	cervix:	n/a	n/a
28	REST	chr2:190648423-190649640	A549	lung:	n/a	chr2:190648965-190648972
29	RUNX3	chr2:190648143-190649877	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:190648130-190649782	GM19099	blood:	n/a	n/a
31	MAZ	chr2:190648242-190649600	HepG2	liver:	n/a	n/a
32	FOXM1	chr2:190648419-190649714	GM12878	blood:	n/a	n/a
33	RCOR1	chr2:190648315-190649746	HepG2	liver:	n/a	n/a
34	TAF1	chr2:190648499-190649585	H1-neurons	neurons:	n/a	n/a
35	SP4	chr2:190648694-190649518	H1-hESC	embryonic stem cell:	n/a	chr2:190649162-190649173 chr2:190648765-190648781
36	POLR2A	chr2:190648221-190649731	GM15510	blood:	n/a	n/a
37	CCNT2	chr2:190648513-190649660	K562	blood:	n/a	n/a
38	POLR2A	chr2:190648309-190649935	K562	blood:	n/a	n/a
39	HEY1	chr2:190648550-190649612	K562	blood:	n/a	n/a
40	ZNF143	chr2:190648534-190649492	H1-hESC	embryonic stem cell:	n/a	chr2:190649435-190649453 chr2:190649071-190649081
41	YY1	chr2:190648503-190649473	GM12878	blood:	n/a	n/a
42	TCF7L2	chr2:190648364-190649564	Hela-S3	cervix:	n/a	n/a
43	PML	chr2:190648671-190649548	K562	blood:	n/a	n/a
44	TAF7	chr2:190648509-190649127	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr2:190648680-190648830	HepG2	liver:	n/a	n/a
46	MAX	chr2:190648089-190650035	A549	lung:	n/a	chr2:190649600-190649609
47	ZBTB7A	chr2:190648511-190649199	HepG2	liver:	n/a	chr2:190648834-190648843 chr2:190648770-190648777
48	SP1	chr2:190648384-190649805	HCT-116	colon:	n/a	chr2:190648772-190648786 chr2:190649162-190649173 chr2:190648569-190648582
49	POLR2A	chr2:190648158-190649707	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr2:190648321-190649799	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:190632138..190639565-chr2:190646675..190650810,8	K562	blood:
2	chr2:190648263..190649127-chr7:48128850..48129707,2	Hela-S3	cervix:
3	chr2:190524918..190527666-chr2:190648010..190650648,4	MCF-7	breast:
4	chr2:190640380..190645016-chr2:190647065..190650284,8	MCF-7	breast:
5	chr2:190648597..190649452-chr5:168006218..168006771,2	Hela-S3	cervix:
6	chr2:190648522..190649281-chr7:27224530..27225300,2	Hela-S3	cervix:
7	chr2:190615675..190618614-chr2:190648414..190651811,3	K562	blood:
8	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
9	chr2:190524324..190528374-chr2:190645867..190651485,5	K562	blood:
10	chr2:190523468..190528374-chr2:190647262..190651485,5	K562	blood:
11	chr2:190624834..190631096-chr2:190647637..190651740,7	K562	blood:
12	chr2:190624834..190630334-chr2:190647529..190650706,8	K562	blood:
13	chr2:190648296..190649291-chr7:129709820..129710568,2	HCT-116	colon:
14	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
15	chr2:190648601..190649551-chr6:2841329..2842193,2	Hela-S3	cervix:
16	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:
17	chr2:190636758..190640017-chr2:190647080..190650145,3	MCF-7	breast:

Variant related genes	Relation type
ORMDL1	TF binding region
PMS1	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000273240	Chromatin interaction
ENSG00000183696	Chromatin interaction
ENSG00000223249	Chromatin interaction
ENSG00000120137	Chromatin interaction
ENSG00000231145	Chromatin interaction
ENSG00000005073	Chromatin interaction
ENSG00000128607	Chromatin interaction
ENSG00000138381	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000240990	Chromatin interaction
ENSG00000021355	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16831821	0.81[EUR][1000 genomes]
rs16831873	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16831944	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16831972	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17271246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164830	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2278591	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289405	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56137655	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56324258	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5742985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743047	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5743072	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs5743077	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62183651	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62183652	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62183653	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62183656	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62183658	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62183659	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62184265	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62184267	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62184268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62184285	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62185869	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62185872	0.89[EUR][1000 genomes]
rs62185874	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62185897	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6748102	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753164	1.00[JPT][hapmap]
rs72920421	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5742926	ORMDL1	cis	Muscle Skeletal	GTEx
rs5742926	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs5742926	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs5742926	PMS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190647000-190650200	Active TSS	Psoas Muscle	Psoas
2	chr2:190647200-190649000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:190647200-190650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:190647400-190649600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:190647400-190649800	Active TSS	Aorta	Aorta
6	chr2:190647400-190650200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:190647400-190650600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr2:190647400-190651200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:190647600-190649600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:190647600-190649800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:190647600-190649800	Active TSS	Fetal Kidney	kidney
12	chr2:190647600-190649800	Active TSS	Hela-S3	cervix
13	chr2:190647600-190649800	Active TSS	HSMMtube	muscle
14	chr2:190647600-190650000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:190647600-190650000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:190647600-190650000	Active TSS	Fetal Intestine Small	intestine
17	chr2:190647600-190650000	Active TSS	Fetal Muscle Leg	muscle
18	chr2:190647600-190650000	Active TSS	A549	lung
19	chr2:190647600-190650000	Active TSS	HMEC	breast
20	chr2:190647600-190650200	Active TSS	Right Ventricle	heart
21	chr2:190647600-190650200	Active TSS	GM12878-XiMat	blood
22	chr2:190647600-190650200	Active TSS	HSMM	muscle
23	chr2:190647600-190650400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:190647600-190650400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:190647600-190650400	Active TSS	K562	blood
26	chr2:190647600-190650400	Active TSS	NHDF-Ad	bronchial
27	chr2:190647600-190650600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:190647600-190650600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:190647600-190650600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr2:190647600-190650600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr2:190647600-190650600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr2:190647600-190650600	Active TSS	NHLF	lung
33	chr2:190647600-190651000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:190647800-190649400	Active TSS	Fetal Thymus	thymus
35	chr2:190647800-190649600	Active TSS	Primary monocytes fromperipheralblood	blood
36	chr2:190647800-190649600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:190647800-190649600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr2:190647800-190649600	Active TSS	Thymus	Thymus
39	chr2:190647800-190649800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr2:190647800-190650000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr2:190647800-190650000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:190647800-190650000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:190647800-190650000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr2:190647800-190650000	Active TSS	Primary T cells fromperipheralblood	blood
45	chr2:190647800-190650000	Active TSS	Colon Smooth Muscle	Colon
46	chr2:190647800-190650000	Active TSS	Fetal Intestine Large	intestine
47	chr2:190647800-190650000	Active TSS	Fetal Stomach	stomach
48	chr2:190647800-190650000	Bivalent/Poised TSS	HepG2	liver
49	chr2:190647800-190650200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:190647800-190650200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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