Variant report

Variant	rs5742923
Chromosome Location	chr2:190648503-190648504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:304)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:304 , 50 per page) page: 1 2 3 4 5 6 7

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	BRCA1	chr2:190648444-190649610	HepG2	liver:	n/a	n/a
8	MYC	chr2:190648093-190649751	K562	blood:	n/a	chr2:190649600-190649609
9	MYC	chr2:190648303-190649722	K562	blood:	n/a	chr2:190649600-190649609
10	MTA3	chr2:190648078-190648734	GM12878	blood:	n/a	n/a
11	GABPA	chr2:190647878-190649564	A549	lung:	n/a	chr2:190649206-190649217
12	PML	chr2:190648447-190649698	GM12878	blood:	n/a	n/a
13	TEAD4	chr2:190647929-190648585	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:190647979-190649869	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr2:190648434-190649600	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:190648112-190650548	H1-hESC	embryonic stem cell:	n/a	n/a
17	EP300	chr2:190648311-190649448	HepG2	liver:	n/a	n/a
18	EBF1	chr2:190648462-190649301	GM12878	blood:	n/a	n/a
19	GABPA	chr2:190647952-190649551	SK-N-SH	brain:	n/a	chr2:190649206-190649217
20	REST	chr2:190648423-190649640	A549	lung:	n/a	chr2:190648965-190648972
21	RUNX3	chr2:190648143-190649877	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:190648130-190649782	GM19099	blood:	n/a	n/a
23	MAZ	chr2:190648242-190649600	HepG2	liver:	n/a	n/a
24	FOXM1	chr2:190648419-190649714	GM12878	blood:	n/a	n/a
25	RCOR1	chr2:190648315-190649746	HepG2	liver:	n/a	n/a
26	TAF1	chr2:190648499-190649585	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr2:190648221-190649731	GM15510	blood:	n/a	n/a
28	POLR2A	chr2:190648309-190649935	K562	blood:	n/a	n/a
29	YY1	chr2:190648503-190649473	GM12878	blood:	n/a	n/a
30	TCF7L2	chr2:190648364-190649564	Hela-S3	cervix:	n/a	n/a
31	MAX	chr2:190648089-190650035	A549	lung:	n/a	chr2:190649600-190649609
32	SP1	chr2:190648384-190649805	HCT-116	colon:	n/a	chr2:190648772-190648786 chr2:190649162-190649173 chr2:190648569-190648582
33	POLR2A	chr2:190648158-190649707	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr2:190648321-190649799	H1-hESC	embryonic stem cell:	n/a	n/a
35	GABPA	chr2:190647896-190649533	HL-60	blood:	n/a	chr2:190649206-190649217
36	STAT5A	chr2:190648077-190648772	GM12878	blood:	n/a	chr2:190648228-190648236
37	MAX	chr2:190648193-190650137	NB4	blood:	n/a	chr2:190649600-190649609
38	CEBPB	chr2:190648347-190649648	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:190648129-190649974	Raji	blood:	n/a	n/a
40	E2F4	chr2:190648425-190649787	MCF10A-Er-Src	breast:	n/a	chr2:190648452-190648466 chr2:190649436-190649448
41	POLR2A	chr2:190648501-190649598	HepG2	liver:	n/a	n/a
42	MAX	chr2:190648014-190650024	HepG2	liver:	n/a	chr2:190649600-190649609
43	EP300	chr2:190648357-190649623	GM12878	blood:	n/a	n/a
44	EBF1	chr2:190648386-190649440	GM12878	blood:	n/a	n/a
45	SIN3A	chr2:190648165-190649894	H1-hESC	embryonic stem cell:	n/a	chr2:190649195-190649206 chr2:190649425-190649438
46	POLR2A	chr2:190648009-190649772	U87	brain:	n/a	n/a
47	TAF1	chr2:190648449-190649016	GM12878	blood:	n/a	n/a
48	CTCF	chr2:190648440-190648590	HMEC	breast:	n/a	chr2:190648467-190648480 chr2:190648554-190648562
49	HEY1	chr2:190648431-190649692	K562	blood:	n/a	n/a
50	MAX	chr2:190648501-190649789	SK-N-SH	brain:	n/a	chr2:190649600-190649609

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:190648463-190648513	T-47D	breast:	n/a
2	chr2:190648463-190648513	U87	brain:	n/a
3	chr2:190648463-190648513	AG09309	skin:	n/a
4	chr2:190648463-190648513	HUVEC	blood vessel:	n/a
5	chr2:190648463-190648513	AG09319	gingival:	n/a
6	chr2:190648463-190648513	AG04450	lung:	fetal
7	chr2:190648463-190648513	NB4	blood:	n/a
8	chr2:190648463-190648513	HCF	heart:	n/a
9	chr2:190648463-190648513	BE2_C	brain:	n/a
10	chr2:190648463-190648513	GM12878	blood:	n/a
11	chr2:190648463-190648513	GM19239	blood:	n/a
12	chr2:190648463-190648513	HCT-116	colon:	n/a
13	chr2:190648463-190648513	H1-hESC	embryonic stem cell:	embryo
14	chr2:190648463-190648513	PANC-1	pancreas:	n/a
15	chr2:190648463-190648513	GM12892	blood:	n/a
16	chr2:190648463-190648513	K562	blood:	n/a
17	chr2:190648463-190648513	Caco-2	colon:	n/a
18	chr2:190648463-190648513	MCF-7	breast:	n/a
19	chr2:190648463-190648513	GM12891	blood:	n/a
20	chr2:190648463-190648513	GM06990	blood:	n/a
21	chr2:190648463-190648513	MCF10A-Er-Src	breast:	n/a
22	chr2:190648463-190648513	HPAEpiC	pulmonary alveolar:	n/a
23	chr2:190648463-190648513	Hela-S3	cervix:	n/a
24	chr2:190648463-190648513	HEEpiC	esophagus:	n/a
25	chr2:190648463-190648513	HCPEpiC	choroid plexus:	n/a
26	chr2:190648463-190648513	IMR90	lung:	fetal
27	chr2:190648463-190648513	LNCaP	prostate:	n/a
28	chr2:190648463-190648513	Hepatocyte	liver:	n/a
29	chr2:190648463-190648513	HRE	kidney:	n/a
30	chr2:190648463-190648513	NHDF-neo	bronchial:	n/a
31	chr2:190648463-190648513	SK-N-MC	brain:	n/a
32	chr2:190648463-190648513	Jurkat	blood:	n/a
33	chr2:190648463-190648513	BJ	skin:	n/a
34	chr2:190648463-190648513	AG04449	skin:	fetal
35	chr2:190648463-190648513	SK-N-SH_RA	brain:	n/a
36	chr2:190648463-190648513	HEK293	kidney:	embryo
37	chr2:190648463-190648513	NT2-D1	testis:	n/a
38	chr2:190648463-190648513	HCM	heart:	n/a
39	chr2:190648463-190648513	HRPEpiC	eye:	n/a
40	chr2:190648463-190648513	SAEC	small airway:	n/a
41	chr2:190648463-190648513	AG10803	skin:	n/a
42	chr2:190648463-190648513	PFSK-1	brain:	n/a
43	chr2:190648463-190648513	HL-60	blood:	n/a
44	chr2:190648463-190648513	HAEpiC	amniotic membrane:	n/a
45	chr2:190648463-190648513	HIPEpiC	eye:	n/a
46	chr2:190648463-190648513	ovcar-3	ovarian:	n/a
47	chr2:190648463-190648513	HepG2	liver:	n/a
48	chr2:190648463-190648513	NHBE	bronchial:	n/a
49	chr2:190648463-190648513	HRCEpiC	kidney:	n/a
50	chr2:190648463-190648513	RPTEC	kidney:	n/a

(count:15 , 50 per page) page: 1

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	chr2:190615675..190618614-chr2:190648414..190651811,3	K562	blood:
6	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
7	chr2:190648081..190648767-chr6:26103962..26104723,2	Hela-S3	cervix:
8	chr2:190524324..190528374-chr2:190645867..190651485,5	K562	blood:
9	chr2:190523468..190528374-chr2:190647262..190651485,5	K562	blood:
10	chr2:190624834..190631096-chr2:190647637..190651740,7	K562	blood:
11	chr2:190624834..190630334-chr2:190647529..190650706,8	K562	blood:
12	chr2:190648296..190649291-chr7:129709820..129710568,2	HCT-116	colon:
13	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
14	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:
15	chr2:190636758..190640017-chr2:190647080..190650145,3	MCF-7	breast:

No data

Variant related genes	Relation type
PMS1	TF binding region
ORMDL1	TF binding region
ORMDL1	CpG island
PMS1	CpG island
ENSG00000223249	Chromatin interaction
ENSG00000231145	Chromatin interaction
ENSG00000273240	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000183696	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000138381	Chromatin interaction
ENSG00000128607	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10176506	1.00[AMR][1000 genomes]
rs10197551	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197577	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10497706	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404356	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411095	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416709	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418043	0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418158	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429804	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831975	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2118453	0.88[AFR][1000 genomes]
rs5742932	1.00[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742935	1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742979	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743009	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs5743026	0.83[AFR][1000 genomes]
rs5743042	0.83[AFR][1000 genomes]
rs5743064	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs5743075	0.84[YRI][hapmap]
rs5743176	0.85[YRI][hapmap]
rs57785091	0.88[AFR][1000 genomes]
rs6711817	0.88[AFR][1000 genomes]
rs6746951	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760126	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048418	0.88[AFR][1000 genomes]
rs73048420	0.88[AFR][1000 genomes]
rs73048432	0.88[AFR][1000 genomes]
rs73048437	0.88[AFR][1000 genomes]
rs73048445	0.91[AFR][1000 genomes]
rs73049960	0.87[AFR][1000 genomes]
rs73050376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7560735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7577159	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs7583918	1.00[AMR][1000 genomes]
rs7600993	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5742923	PMS1	cis	multi-tissue	Pritchard
rs5742923	PMS1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190647000-190648800	Active TSS	Right Atrium	heart
2	chr2:190647000-190650200	Active TSS	Psoas Muscle	Psoas
3	chr2:190647200-190648600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:190647200-190649000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:190647200-190650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:190647400-190648600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:190647400-190649600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:190647400-190649800	Active TSS	Aorta	Aorta
9	chr2:190647400-190650200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:190647400-190650600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:190647400-190651200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:190647600-190648600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr2:190647600-190648600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:190647600-190649600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:190647600-190649800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:190647600-190649800	Active TSS	Fetal Kidney	kidney
17	chr2:190647600-190649800	Active TSS	Hela-S3	cervix
18	chr2:190647600-190649800	Active TSS	HSMMtube	muscle
19	chr2:190647600-190650000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr2:190647600-190650000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:190647600-190650000	Active TSS	Fetal Intestine Small	intestine
22	chr2:190647600-190650000	Active TSS	Fetal Muscle Leg	muscle
23	chr2:190647600-190650000	Active TSS	A549	lung
24	chr2:190647600-190650000	Active TSS	HMEC	breast
25	chr2:190647600-190650200	Active TSS	Right Ventricle	heart
26	chr2:190647600-190650200	Active TSS	GM12878-XiMat	blood
27	chr2:190647600-190650200	Active TSS	HSMM	muscle
28	chr2:190647600-190650400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:190647600-190650400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:190647600-190650400	Active TSS	K562	blood
31	chr2:190647600-190650400	Active TSS	NHDF-Ad	bronchial
32	chr2:190647600-190650600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:190647600-190650600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr2:190647600-190650600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr2:190647600-190650600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:190647600-190650600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:190647600-190650600	Active TSS	NHLF	lung
38	chr2:190647600-190651000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:190647800-190649400	Active TSS	Fetal Thymus	thymus
40	chr2:190647800-190649600	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr2:190647800-190649600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:190647800-190649600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr2:190647800-190649600	Active TSS	Thymus	Thymus
44	chr2:190647800-190649800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr2:190647800-190650000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr2:190647800-190650000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:190647800-190650000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:190647800-190650000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr2:190647800-190650000	Active TSS	Primary T cells fromperipheralblood	blood
50	chr2:190647800-190650000	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links