Variant report

Variant	rs743974
Chromosome Location	chrX:54834957-54834958
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	SIN3A	chrX:54834048-54835955	H1-hESC	embryonic stem cell:	n/a	chrX:54834132-54834145
2	POLR2A	chrX:54834954-54835773	Hela-S3	cervix:	n/a	n/a
3	TAF7	chrX:54834876-54835000	K562	blood:	n/a	n/a
4	GABPA	chrX:54834452-54835159	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chrX:54834679-54835736	GM19193	blood:	n/a	n/a
6	MAX	chrX:54834945-54835589	Hela-S3	cervix:	n/a	chrX:54835372-54835382
7	TCF7L2	chrX:54834637-54835617	HCT-116	colon:	n/a	chrX:54835386-54835400 chrX:54835388-54835397 chrX:54835385-54835399 chrX:54835385-54835401
8	POLR2A	chrX:54834656-54835685	HEK293	kidney:	n/a	n/a
9	FOXA1	chrX:54834863-54835236	T-47D	breast:	n/a	n/a
10	KAP1	chrX:54834173-54835320	HEK293	kidney:	n/a	n/a
11	ZNF143	chrX:54834770-54835546	GM12878	blood:	n/a	chrX:54834847-54834856
12	TBP	chrX:54834885-54835271	K562	blood:	n/a	n/a
13	POLR2A	chrX:54834574-54835931	MCF-7	breast:	n/a	n/a
14	POLR2A	chrX:54834723-54834972	A549	lung:	n/a	n/a
15	MAZ	chrX:54833814-54836035	IMR90	lung:	n/a	chrX:54834112-54834122
16	RFX5	chrX:54834766-54835716	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chrX:54833948-54835715	H1-neurons	neurons:	n/a	n/a
18	RCOR1	chrX:54834187-54835676	K562	blood:	n/a	n/a
19	NRF1	chrX:54834809-54835652	SK-N-SH	brain:	n/a	chrX:54835292-54835306 chrX:54835370-54835379 chrX:54835451-54835460 chrX:54835449-54835460 chrX:54835417-54835426 chrX:54835295-54835304 chrX:54835449-54835458 chrX:54835295-54835309 chrX:54835370-54835381 chrX:54835446-54835460 chrX:54835449-54835463 chrX:54835297-54835306 chrX:54835295-54835306 chrX:54835370-54835381 chrX:54835367-54835381
20	POLR2A	chrX:54834673-54835777	GM12878	blood:	n/a	n/a
21	GATA3	chrX:54834721-54835212	T-47D	breast:	n/a	n/a
22	STAT1	chrX:54834312-54835009	GM12878	blood:	n/a	chrX:54834567-54834579 chrX:54834979-54834991 chrX:54834721-54834733
23	POLR2A	chrX:54834679-54835741	K562	blood:	n/a	n/a
24	POLR2A	chrX:54834686-54835706	GM15510	blood:	n/a	n/a
25	CTCF	chrX:54834840-54834990	SK-N-SH_RA	brain:	n/a	chrX:54834913-54834926
26	MAZ	chrX:54834607-54835594	HepG2	liver:	n/a	n/a
27	POLR2A	chrX:54834634-54835029	SK-N-SH	brain:	n/a	n/a
28	CTCF	chrX:54834956-54835000	H1-hESC	embryonic stem cell:	n/a	n/a
29	GABPA	chrX:54834457-54835103	A549	lung:	n/a	n/a
30	TCF12	chrX:54834442-54835217	A549	lung:	n/a	n/a
31	ELF1	chrX:54834562-54834984	K562	blood:	n/a	chrX:54834777-54834790
32	TBP	chrX:54834834-54834962	GM12878	blood:	n/a	n/a
33	TAF1	chrX:54834654-54834994	H1-hESC	embryonic stem cell:	n/a	n/a
34	BACH1	chrX:54834812-54835063	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chrX:54834516-54835847	PFSK-1	brain:	n/a	n/a
36	POLR2A	chrX:54834832-54834981	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chrX:54834592-54836220	HepG2	liver:	n/a	n/a
38	POLR2A	chrX:54834730-54835822	GM12878	blood:	n/a	n/a
39	GABPA	chrX:54834491-54835045	MCF-7	breast:	n/a	n/a
40	POLR2A	chrX:54834731-54836246	IMR90	lung:	n/a	n/a
41	MXI1	chrX:54834460-54836368	IMR90	lung:	n/a	n/a
42	CTCF	chrX:54834820-54834970	BE2_C	brain:	n/a	chrX:54834913-54834926
43	MAZ	chrX:54833918-54835922	K562	blood:	n/a	chrX:54834112-54834122
44	JUND	chrX:54834370-54835133	H1-hESC	embryonic stem cell:	n/a	chrX:54834629-54834641
45	POLR2A	chrX:54834785-54835841	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chrX:54834789-54835902	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chrX:54834562-54835823	H1-hESC	embryonic stem cell:	n/a	n/a
48	CHD2	chrX:54834534-54835699	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chrX:54834051-54836048	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chrX:54834783-54835610	K562	blood:	n/a	chrX:54835372-54835382

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:54834954-54835004	T-47D	breast:	n/a
2	chrX:54834954-54835004	AG04449	skin:	fetal
3	chrX:54834954-54835004	LNCaP	prostate:	n/a
4	chrX:54834954-54835004	NH-A	brain:	n/a
5	chrX:54834954-54835004	HEK293	kidney:	embryo
6	chrX:54834954-54835004	SK-N-SH_RA	brain:	n/a
7	chrX:54834954-54835004	HUVEC	blood vessel:	n/a
8	chrX:54834954-54835004	HCF	heart:	n/a
9	chrX:54834954-54835004	SK-N-MC	brain:	n/a
10	chrX:54834954-54835004	AG04450	lung:	fetal
11	chrX:54834954-54835004	GM19239	blood:	n/a
12	chrX:54834954-54835004	HEEpiC	esophagus:	n/a
13	chrX:54834954-54835004	HRCEpiC	kidney:	n/a
14	chrX:54834954-54835004	IMR90	lung:	fetal
15	chrX:54834954-54835004	AG09309	skin:	n/a
16	chrX:54834954-54835004	SK-N-SH	brain:	n/a
17	chrX:54834954-54835004	HRPEpiC	eye:	n/a
18	chrX:54834954-54835004	BJ	skin:	n/a
19	chrX:54834954-54835004	Jurkat	blood:	n/a
20	chrX:54834954-54835004	ECC-1	luminal epithelium:	n/a
21	chrX:54834954-54835004	HCT-116	colon:	n/a
22	chrX:54834954-54835004	AG10803	skin:	n/a
23	chrX:54834954-54835004	GM06990	blood:	n/a
24	chrX:54834954-54835004	BE2_C	brain:	n/a
25	chrX:54834954-54835004	NB4	blood:	n/a
26	chrX:54834954-54835004	NT2-D1	testis:	n/a
27	chrX:54834954-54835004	HAEpiC	amniotic membrane:	n/a
28	chrX:54834954-54835004	HL-60	blood:	n/a
29	chrX:54834954-54835004	MCF10A-Er-Src	breast:	n/a
30	chrX:54834954-54835004	HPAEpiC	pulmonary alveolar:	n/a
31	chrX:54834954-54835004	K562	blood:	n/a
32	chrX:54834954-54835004	SKMC	muscle:	n/a
33	chrX:54834954-54835004	HMEC	breast:	n/a
34	chrX:54834954-54835004	PrEC	prostate:	n/a
35	chrX:54834954-54835004	HCM	heart:	n/a
36	chrX:54834954-54835004	PFSK-1	brain:	n/a
37	chrX:54834954-54835004	HNPCEpiC	eye:	n/a
38	chrX:54834954-54835004	NHDF-neo	bronchial:	n/a
39	chrX:54834954-54835004	ovcar-3	ovarian:	n/a
40	chrX:54834954-54835004	HIPEpiC	eye:	n/a
41	chrX:54834954-54835004	AG09319	gingival:	n/a
42	chrX:54834954-54835004	NHBE	bronchial:	n/a
43	chrX:54834954-54835004	H1-hESC	embryonic stem cell:	embryo
44	chrX:54834954-54835004	AoSMC	blood vessel:	n/a
45	chrX:54834954-54835004	SAEC	small airway:	n/a
46	chrX:54834954-54835004	HCPEpiC	choroid plexus:	n/a
47	chrX:54834954-54835004	Hepatocyte	liver:	n/a
48	chrX:54834954-54835004	GM12892	blood:	n/a
49	chrX:54834954-54835004	RPTEC	kidney:	n/a
50	chrX:54834954-54835004	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:54822974..54825494-chrX:54833093..54835325,2	MCF-7	breast:
2	chrX:54820960..54826287-chrX:54830862..54836131,8	MCF-7	breast:

Variant related genes	Relation type
MAGED2	TF binding region
MAGED2	CpG island
ENSG00000102313	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1043031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs1043034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs1043044	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs12014660	0.84[CEU][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap]
rs12832165	0.80[CEU][hapmap]
rs12851962	0.94[CEU][hapmap];0.91[TSI][hapmap]
rs12858090	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs12858147	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap]
rs2005463	0.84[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2071932	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs2071933	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs2071934	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2273138	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs2281383	0.94[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2361189	1.00[CEU][hapmap]
rs3765479	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs4826364	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap]
rs4826365	0.84[CEU][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap]
rs5914241	0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs5960055	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs5960336	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs6611391	0.94[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs763183	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs763184	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs743974	MAGED2	cis	brain	BrainEAC
rs743974	MAGED2	cis	temporal cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:54833600-54835800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chrX:54833600-54836200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chrX:54833800-54835600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chrX:54833800-54835600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chrX:54833800-54835600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chrX:54833800-54835600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chrX:54833800-54835600	Active TSS	Fetal Lung	lung
8	chrX:54833800-54835600	Active TSS	Fetal Muscle Leg	muscle
9	chrX:54833800-54835800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chrX:54833800-54836000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chrX:54833800-54836200	Active TSS	H1 Cell Line	embryonic stem cell
12	chrX:54833800-54836200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chrX:54833800-54836200	Active TSS	Fetal Kidney	kidney
14	chrX:54833800-54836400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chrX:54834000-54835000	Active TSS	Fetal Brain Male	brain
16	chrX:54834000-54835200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
17	chrX:54834000-54835400	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chrX:54834000-54835600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chrX:54834000-54835600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chrX:54834000-54835600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chrX:54834000-54835600	Active TSS	Fetal Thymus	thymus
22	chrX:54834000-54835600	Active TSS	Left Ventricle	heart
23	chrX:54834000-54835600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chrX:54834000-54835800	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chrX:54834000-54835800	Active TSS	Brain Angular Gyrus	brain
26	chrX:54834000-54835800	Active TSS	Brain Germinal Matrix	brain
27	chrX:54834000-54835800	Active TSS	Brain Hippocampus Middle	brain
28	chrX:54834000-54835800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chrX:54834000-54835800	Active TSS	Duodenum Mucosa	Duodenum
30	chrX:54834000-54835800	Active TSS	Fetal Intestine Large	intestine
31	chrX:54834000-54835800	Active TSS	Fetal Intestine Small	intestine
32	chrX:54834000-54835800	Active TSS	Right Atrium	heart
33	chrX:54834000-54835800	Active TSS	Right Ventricle	heart
34	chrX:54834000-54836000	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chrX:54834000-54836000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chrX:54834000-54836000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chrX:54834000-54836000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chrX:54834000-54836000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chrX:54834000-54836000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chrX:54834000-54836000	Active TSS	Brain Anterior Caudate	brain
41	chrX:54834000-54836000	Active TSS	Thymus	Thymus
42	chrX:54834000-54836000	Active TSS	HSMMtube	muscle
43	chrX:54834000-54836200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chrX:54834000-54836200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chrX:54834000-54836200	Active TSS	Ovary	ovary
46	chrX:54834000-54836200	Active TSS	Placenta Amnion	Placenta Amnion
47	chrX:54834000-54836200	Active TSS	HUVEC	blood vessel
48	chrX:54834000-54836400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chrX:54834000-54836400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chrX:54834000-54836400	Active TSS	HUES64 Cell Line	embryonic stem cell

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