Variant report

Variant	rs5742934
Chromosome Location	chr2:190649393-190649394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:426)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:426 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

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	BRCA1	chr2:190648444-190649610	HepG2	liver:	n/a	n/a
9	MYC	chr2:190648093-190649751	K562	blood:	n/a	chr2:190649600-190649609
10	MYC	chr2:190648303-190649722	K562	blood:	n/a	chr2:190649600-190649609
11	BRCA1	chr2:190648802-190649664	Hela-S3	cervix:	n/a	n/a
12	E2F6	chr2:190648560-190649795	H1-hESC	embryonic stem cell:	n/a	chr2:190649437-190649448 chr2:190649436-190649448
13	GABPA	chr2:190647878-190649564	A549	lung:	n/a	chr2:190649206-190649217
14	TAL1	chr2:190648860-190649456	K562	blood:	n/a	n/a
15	HA-E2F1	chr2:190648527-190649636	Hela-S3	cervix:	n/a	chr2:190649198-190649209 chr2:190649436-190649448
16	POLR2A	chr2:190648524-190649546	A549	lung:	n/a	n/a
17	PML	chr2:190648447-190649698	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:190647979-190649869	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr2:190648434-190649600	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:190648112-190650548	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr2:190648311-190649448	HepG2	liver:	n/a	n/a
22	REST	chr2:190648516-190649530	SK-N-SH	brain:	n/a	chr2:190648965-190648972
23	GABPA	chr2:190647952-190649551	SK-N-SH	brain:	n/a	chr2:190649206-190649217
24	TBP	chr2:190648693-190649911	Hela-S3	cervix:	n/a	n/a
25	REST	chr2:190648423-190649640	A549	lung:	n/a	chr2:190648965-190648972
26	RUNX3	chr2:190648143-190649877	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:190648130-190649782	GM19099	blood:	n/a	n/a
28	MAZ	chr2:190648242-190649600	HepG2	liver:	n/a	n/a
29	CHD1	chr2:190649217-190650125	H1-hESC	embryonic stem cell:	n/a	n/a
30	FOXM1	chr2:190648419-190649714	GM12878	blood:	n/a	n/a
31	RCOR1	chr2:190648315-190649746	HepG2	liver:	n/a	n/a
32	TAF1	chr2:190648499-190649585	H1-neurons	neurons:	n/a	n/a
33	SP4	chr2:190648694-190649518	H1-hESC	embryonic stem cell:	n/a	chr2:190649162-190649173 chr2:190648765-190648781
34	POLR2A	chr2:190648221-190649731	GM15510	blood:	n/a	n/a
35	CCNT2	chr2:190648513-190649660	K562	blood:	n/a	n/a
36	MYC	chr2:190648874-190649481	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:190648309-190649935	K562	blood:	n/a	n/a
38	HEY1	chr2:190648550-190649612	K562	blood:	n/a	n/a
39	ZNF143	chr2:190648534-190649492	H1-hESC	embryonic stem cell:	n/a	chr2:190649435-190649453 chr2:190649071-190649081
40	YY1	chr2:190648503-190649473	GM12878	blood:	n/a	n/a
41	TCF7L2	chr2:190648364-190649564	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr2:190649320-190649470	HBMEC	blood vessel:	n/a	n/a
43	PML	chr2:190648671-190649548	K562	blood:	n/a	n/a
44	SIN3AK20	chr2:190648913-190649393	PFSK-1	brain:	n/a	n/a
45	RAD21	chr2:190648967-190649684	IMR90	lung:	n/a	n/a
46	MAX	chr2:190648089-190650035	A549	lung:	n/a	chr2:190649600-190649609
47	SP1	chr2:190648384-190649805	HCT-116	colon:	n/a	chr2:190648772-190648786 chr2:190649162-190649173 chr2:190648569-190648582
48	POLR2A	chr2:190648158-190649707	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr2:190648321-190649799	H1-hESC	embryonic stem cell:	n/a	n/a
50	GABPA	chr2:190647896-190649533	HL-60	blood:	n/a	chr2:190649206-190649217

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:190649374-190649424	MCF10A-Er-Src	breast:	n/a
2	chr2:190649374-190649424	MCF-7	breast:	n/a
3	chr2:190649374-190649424	SAEC	small airway:	n/a
4	chr2:190649374-190649424	NHDF-neo	bronchial:	n/a
5	chr2:190649374-190649424	HEK293	kidney:	embryo
6	chr2:190649374-190649424	HepG2	liver:	n/a
7	chr2:190649374-190649424	LNCaP	prostate:	n/a
8	chr2:190649374-190649424	Hepatocyte	liver:	n/a
9	chr2:190649374-190649424	SK-N-MC	brain:	n/a
10	chr2:190649374-190649424	Hela-S3	cervix:	n/a
11	chr2:190649374-190649424	HEEpiC	esophagus:	n/a
12	chr2:190649374-190649424	AG04449	skin:	fetal
13	chr2:190649374-190649424	HCPEpiC	choroid plexus:	n/a
14	chr2:190649374-190649424	GM06990	blood:	n/a
15	chr2:190649374-190649424	HRPEpiC	eye:	n/a
16	chr2:190649374-190649424	GM12891	blood:	n/a
17	chr2:190649374-190649424	BE2_C	brain:	n/a
18	chr2:190649374-190649424	AG04450	lung:	fetal
19	chr2:190649374-190649424	BJ	skin:	n/a
20	chr2:190649374-190649424	NT2-D1	testis:	n/a
21	chr2:190649374-190649424	PFSK-1	brain:	n/a
22	chr2:190649374-190649424	ovcar-3	ovarian:	n/a
23	chr2:190649374-190649424	K562	blood:	n/a
24	chr2:190649374-190649424	RPTEC	kidney:	n/a
25	chr2:190649374-190649424	AG09319	gingival:	n/a
26	chr2:190649374-190649424	Jurkat	blood:	n/a
27	chr2:190649374-190649424	HCF	heart:	n/a
28	chr2:190649374-190649424	A549	lung:	n/a
29	chr2:190649374-190649424	CMK	blood:	n/a
30	chr2:190649374-190649424	AG10803	skin:	n/a
31	chr2:190649374-190649424	HPAEpiC	pulmonary alveolar:	n/a
32	chr2:190649374-190649424	HCM	heart:	n/a
33	chr2:190649374-190649424	ECC-1	luminal epithelium:	n/a
34	chr2:190649374-190649424	NHBE	bronchial:	n/a
35	chr2:190649374-190649424	SK-N-SH	brain:	n/a
36	chr2:190649374-190649424	GM19239	blood:	n/a
37	chr2:190649374-190649424	HNPCEpiC	eye:	n/a
38	chr2:190649374-190649424	HRE	kidney:	n/a
39	chr2:190649374-190649424	HIPEpiC	eye:	n/a
40	chr2:190649374-190649424	PANC-1	pancreas:	n/a
41	chr2:190649374-190649424	HRCEpiC	kidney:	n/a
42	chr2:190649374-190649424	AG09309	skin:	n/a
43	chr2:190649374-190649424	ProgFib	skin:	n/a
44	chr2:190649374-190649424	Caco-2	colon:	n/a
45	chr2:190649374-190649424	SK-N-SH_RA	brain:	n/a
46	chr2:190649374-190649424	PrEC	prostate:	n/a
47	chr2:190649374-190649424	NB4	blood:	n/a
48	chr2:190649374-190649424	GM12892	blood:	n/a
49	chr2:190649374-190649424	NH-A	brain:	n/a
50	chr2:190649374-190649424	H1-hESC	embryonic stem cell:	embryo

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190632138..190639565-chr2:190646675..190650810,8	K562	blood:
2	chr2:190524918..190527666-chr2:190648010..190650648,4	MCF-7	breast:
3	chr2:190640380..190645016-chr2:190647065..190650284,8	MCF-7	breast:
4	chr2:190648597..190649452-chr5:168006218..168006771,2	Hela-S3	cervix:
5	chr2:190649071..190649611-chr7:7679917..7680683,2	Hela-S3	cervix:
6	chr2:190615675..190618614-chr2:190648414..190651811,3	K562	blood:
7	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
8	chr17:16118765..16119327-chr2:190649095..190649706,2	NB4	blood:
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	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
14	chr2:190648601..190649551-chr6:2841329..2842193,2	Hela-S3	cervix:
15	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:
16	chr2:190617143..190618720-chr2:190648807..190650350,2	MCF-7	breast:
17	chr2:190636758..190640017-chr2:190647080..190650145,3	MCF-7	breast:

No data

Variant related genes	Relation type
ORMDL1	TF binding region
ORMDL1	CpG island
ENSG00000128699	Chromatin interaction
ENSG00000120137	Chromatin interaction
ENSG00000138381	Chromatin interaction
ENSG00000021355	Chromatin interaction
ENSG00000273240	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000231145	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000223249	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11883813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11888192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225076	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225083	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225097	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225100	0.82[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225105	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225119	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225121	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12693550	0.80[YRI][hapmap]
rs1470100	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1898559	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2196670	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2254040	0.80[YRI][hapmap]
rs2352288	0.80[YRI][hapmap]
rs4667301	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs5742925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742929	0.83[AFR][1000 genomes]
rs5742949	0.83[YRI][hapmap]
rs6434362	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs6708086	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6736443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs930426	0.80[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5742934	PMS1	cis	multi-tissue	Pritchard

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	chr2:190647200-190650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:190647400-190649600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:190647400-190649800	Active TSS	Aorta	Aorta
5	chr2:190647400-190650200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:190647400-190650600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:190647400-190651200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:190647600-190649600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:190647600-190649800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:190647600-190649800	Active TSS	Fetal Kidney	kidney
11	chr2:190647600-190649800	Active TSS	Hela-S3	cervix
12	chr2:190647600-190649800	Active TSS	HSMMtube	muscle
13	chr2:190647600-190650000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr2:190647600-190650000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:190647600-190650000	Active TSS	Fetal Intestine Small	intestine
16	chr2:190647600-190650000	Active TSS	Fetal Muscle Leg	muscle
17	chr2:190647600-190650000	Active TSS	A549	lung
18	chr2:190647600-190650000	Active TSS	HMEC	breast
19	chr2:190647600-190650200	Active TSS	Right Ventricle	heart
20	chr2:190647600-190650200	Active TSS	GM12878-XiMat	blood
21	chr2:190647600-190650200	Active TSS	HSMM	muscle
22	chr2:190647600-190650400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:190647600-190650400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:190647600-190650400	Active TSS	K562	blood
25	chr2:190647600-190650400	Active TSS	NHDF-Ad	bronchial
26	chr2:190647600-190650600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:190647600-190650600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr2:190647600-190650600	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:190647600-190650600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:190647600-190650600	Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:190647600-190650600	Active TSS	NHLF	lung
32	chr2:190647600-190651000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:190647800-190649400	Active TSS	Fetal Thymus	thymus
34	chr2:190647800-190649600	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr2:190647800-190649600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:190647800-190649600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:190647800-190649600	Active TSS	Thymus	Thymus
38	chr2:190647800-190649800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr2:190647800-190650000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr2:190647800-190650000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:190647800-190650000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:190647800-190650000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:190647800-190650000	Active TSS	Primary T cells fromperipheralblood	blood
44	chr2:190647800-190650000	Active TSS	Colon Smooth Muscle	Colon
45	chr2:190647800-190650000	Active TSS	Fetal Intestine Large	intestine
46	chr2:190647800-190650000	Active TSS	Fetal Stomach	stomach
47	chr2:190647800-190650000	Bivalent/Poised TSS	HepG2	liver
48	chr2:190647800-190650200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:190647800-190650200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:190647800-190650600	Active TSS	Fetal Brain Female	brain

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