Variant report

Variant	rs57890299
Chromosome Location	chr2:178261828-178261829
allele	A/G
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	FOXA2	chr2:178260768-178263923	HepG2	liver:	n/a	n/a
2	EP300	chr2:178261253-178261874	A549	lung:	n/a	chr2:178261613-178261623 chr2:178261557-178261564
3	MBD4	chr2:178261145-178262174	HepG2	liver:	n/a	n/a
4	GTF3C2	chr2:178261554-178262079	Hela-S3	cervix:	n/a	n/a
5	FOXA2	chr2:178261292-178262006	A549	lung:	n/a	n/a
6	NFIC	chr2:178261289-178262709	SK-N-SH	brain:	n/a	n/a
7	FOXA1	chr2:178261293-178262120	HepG2	liver:	n/a	n/a
8	RPC155	chr2:178261421-178262332	Hela-S3	cervix:	n/a	n/a
9	FOXA1	chr2:178261205-178261910	HepG2	liver:	n/a	n/a
10	TCF12	chr2:178261191-178262924	SK-N-SH	brain:	n/a	chr2:178261613-178261622
11	NFIC	chr2:178261219-178261920	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr2:178261797-178261905	HepG2	liver:	n/a	n/a
13	EP300	chr2:178261303-178261828	HepG2	liver:	n/a	chr2:178261613-178261623 chr2:178261557-178261564
14	NFIC	chr2:178261319-178261930	HepG2	liver:	n/a	n/a
15	FOSL2	chr2:178261261-178261839	HepG2	liver:	n/a	n/a
16	FOSL2	chr2:178261259-178261833	SK-N-SH	brain:	n/a	n/a
17	FOSL2	chr2:178261229-178261851	A549	lung:	n/a	n/a
18	EP300	chr2:178261189-178261937	ECC-1	luminal epithelium:	n/a	chr2:178261613-178261623 chr2:178261557-178261564
19	EP300	chr2:178261307-178261874	HepG2	liver:	n/a	chr2:178261613-178261623 chr2:178261557-178261564
20	POLR2A	chr2:178261064-178261849	HUVEC	blood vessel:	n/a	n/a
21	TEAD4	chr2:178261165-178261907	HepG2	liver:	n/a	chr2:178261570-178261579
22	FOXA1	chr2:178261250-178261874	HepG2	liver:	n/a	n/a
23	MYBL2	chr2:178261161-178262166	HepG2	liver:	n/a	n/a
24	JUND	chr2:178261266-178261857	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:178261006-178261853	HUVEC	blood vessel:	n/a	n/a
26	TEAD4	chr2:178261213-178261828	ECC-1	luminal epithelium:	n/a	chr2:178261570-178261579
27	TCF12	chr2:178261215-178261973	A549	lung:	n/a	chr2:178261613-178261622
28	MYBL2	chr2:178261254-178261940	HepG2	liver:	n/a	n/a
29	SP1	chr2:178261345-178261902	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:178112424..178116788-chr2:178259811..178263251,4	K562	blood:
2	chr2:178125970..178131401-chr2:178255081..178263132,15	K562	blood:
3	chr2:178257565..178262041-chr2:178276576..178279686,5	K562	blood:
4	chr2:178258938..178262041-chr2:178277248..178280629,3	K562	blood:
5	chr2:178202563..178204243-chr2:178260554..178263397,2	K562	blood:
6	chr2:178220224..178223061-chr2:178258523..178262241,3	K562	blood:

Variant related genes	Relation type
ENSG00000213963	TF binding region
NFE2L2	TF binding region
ENSG00000222043	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10172305	0.85[EUR][1000 genomes]
rs10176724	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10180514	0.85[AFR][1000 genomes]
rs10184488	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10190306	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10194452	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10208055	0.83[EUR][1000 genomes]
rs10497504	0.84[AFR][1000 genomes]
rs10497505	0.81[EUR][1000 genomes]
rs10497506	0.81[EUR][1000 genomes]
rs10497509	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10754987	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10754988	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10803911	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10803912	0.84[AFR][1000 genomes]
rs10930788	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10930789	0.88[EUR][1000 genomes]
rs10930790	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10930791	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10930793	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11891003	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12468046	0.83[EUR][1000 genomes]
rs12478545	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12612957	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12621156	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12693121	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12997516	0.83[EUR][1000 genomes]
rs13007779	0.83[EUR][1000 genomes]
rs1345138	0.84[AFR][1000 genomes]
rs1349762	0.86[EUR][1000 genomes]
rs1374438	0.86[AFR][1000 genomes]
rs1446837	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1446838	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1453369	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1530965	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1545363	0.83[EUR][1000 genomes]
rs1584806	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17326999	0.82[EUR][1000 genomes]
rs17398864	0.83[EUR][1000 genomes]
rs1838890	0.84[AFR][1000 genomes]
rs1867905	0.84[AFR][1000 genomes]
rs1901823	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1979059	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2044493	0.83[EUR][1000 genomes]
rs2084966	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2084967	0.83[EUR][1000 genomes]
rs2100395	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2123643	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2141157	0.86[AFR][1000 genomes]
rs2166556	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2166557	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2167902	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2218575	0.84[AFR][1000 genomes]
rs2293475	0.84[AFR][1000 genomes]
rs2364846	0.85[EUR][1000 genomes]
rs2364849	0.88[EUR][1000 genomes]
rs2364850	0.81[EUR][1000 genomes]
rs2364851	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2364852	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3754989	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3813260	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3952496	0.86[EUR][1000 genomes]
rs4243389	0.86[AFR][1000 genomes]
rs4308151	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4335983	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4350784	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4402804	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4585065	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4893822	0.81[AFR][1000 genomes]
rs4893824	0.81[AFR][1000 genomes]
rs4893826	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4893827	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4893829	0.84[AFR][1000 genomes]
rs4893933	0.82[EUR][1000 genomes]
rs4893940	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4893942	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4893943	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4893951	0.81[AFR][1000 genomes]
rs4893955	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4893956	0.86[AFR][1000 genomes]
rs6433664	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6433666	0.81[EUR][1000 genomes]
rs6433674	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6433675	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6433676	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6433677	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6710109	0.86[AFR][1000 genomes]
rs6715365	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6717457	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6719114	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6720483	0.88[EUR][1000 genomes]
rs6721168	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6723014	0.84[AFR][1000 genomes]
rs6725096	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6732250	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6739792	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6741974	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6744488	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6759567	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7568452	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7570297	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7582179	0.84[AFR][1000 genomes]
rs7585952	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7588049	0.84[AFR][1000 genomes]
rs7589927	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7594073	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7601132	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7604299	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7604668	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7607073	0.86[AFR][1000 genomes]
rs7608135	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9288001	0.87[EUR][1000 genomes]
rs935426	0.84[AFR][1000 genomes]
rs9789580	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9917193	0.88[EUR][1000 genomes]
rs9917333	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57890299	AGPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178258400-178262400	Weak transcription	Pancreas	Pancrea
2	chr2:178258400-178262400	Weak transcription	Small Intestine	intestine
3	chr2:178258400-178262800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:178258400-178263000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr2:178258400-178263200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:178258400-178264400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:178258400-178264400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:178258400-178272600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:178258600-178262400	Weak transcription	Fetal Thymus	thymus
10	chr2:178258600-178262600	Weak transcription	Ovary	ovary
11	chr2:178258600-178264000	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:178258600-178264200	Weak transcription	Right Atrium	heart
13	chr2:178258800-178262800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:178258800-178263000	Enhancers	NHEK	skin
15	chr2:178258800-178263400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:178258800-178264000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:178258800-178264400	Enhancers	Stomach Mucosa	stomach
18	chr2:178258800-178277200	Weak transcription	Right Ventricle	heart
19	chr2:178258800-178285000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:178258800-178294200	Weak transcription	Thymus	Thymus
21	chr2:178259000-178262800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:178259000-178262800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:178259000-178263000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:178259000-178264800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr2:178259000-178269000	Weak transcription	Fetal Lung	lung
26	chr2:178259200-178262200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:178259200-178262600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:178259200-178263200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:178259200-178263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:178259400-178262400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:178259400-178263000	Weak transcription	Primary T cells from cord blood	blood
32	chr2:178259400-178263600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:178259400-178263600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:178259400-178264400	Enhancers	Adipose Nuclei	Adipose
35	chr2:178259400-178267400	Weak transcription	Fetal Stomach	stomach
36	chr2:178259600-178263400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:178259600-178264600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr2:178259600-178266000	Enhancers	Liver	Liver
39	chr2:178259800-178263600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:178259800-178265800	Enhancers	Primary hematopoietic stem cells	blood
41	chr2:178259800-178271200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:178260000-178262000	Weak transcription	Fetal Kidney	kidney
43	chr2:178260000-178263400	Enhancers	HMEC	breast
44	chr2:178260200-178262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:178260200-178262400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:178260200-178262400	Weak transcription	Spleen	Spleen
47	chr2:178260200-178262800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:178260200-178263400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:178260200-178268800	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:178260200-178269600	Weak transcription	Brain Anterior Caudate	brain

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