Variant report

Variant	rs38743
Chromosome Location	chr7:140715297-140715298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr7:140714541-140715313	A549	lung:	n/a	chr7:140714872-140714885
2	MAFK	chr7:140713210-140715353	K562	blood:	n/a	chr7:140713536-140713547 chr7:140713536-140713551 chr7:140713536-140713547
3	GABPA	chr7:140713907-140715316	A549	lung:	n/a	chr7:140714897-140714908 chr7:140714897-140714911 chr7:140714899-140714908 chr7:140714894-140714908
4	MXI1	chr7:140712802-140715958	SK-N-SH	brain:	n/a	chr7:140714240-140714249
5	CTCF	chr7:140713723-140715658	SK-N-SH	brain:	n/a	chr7:140715489-140715496
6	RCOR1	chr7:140714215-140715343	K562	blood:	n/a	n/a
7	CBX3	chr7:140713886-140715463	K562	blood:	n/a	n/a
8	PML	chr7:140713930-140715364	GM12878	blood:	n/a	n/a
9	ZEB1	chr7:140714417-140715316	GM12878	blood:	n/a	n/a
10	CUX1	chr7:140714289-140715529	K562	blood:	n/a	n/a
11	MTA3	chr7:140713853-140715348	GM12878	blood:	n/a	n/a
12	RCOR1	chr7:140714016-140715341	GM12878	blood:	n/a	n/a
13	MXI1	chr7:140713703-140715393	IMR90	lung:	n/a	chr7:140714240-140714249
14	GATA3	chr7:140714949-140715326	SH-SY5Y	brain:	n/a	n/a
15	GATA2	chr7:140714113-140715346	SH-SY5Y	brain:	n/a	n/a
16	SIN3AK20	chr7:140714082-140715400	MCF-7	breast:	n/a	n/a
17	CTCF	chr7:140713793-140715720	A549	lung:	n/a	chr7:140715489-140715496
18	TAF1	chr7:140714095-140715364	ECC-1	luminal epithelium:	n/a	n/a
19	MYC	chr7:140713824-140715428	K562	blood:	n/a	n/a
20	POLR2A	chr7:140713551-140715393	SK-N-MC	brain:	n/a	n/a
21	MAX	chr7:140713939-140715321	A549	lung:	n/a	n/a
22	MAX	chr7:140713987-140715329	HCT-116	colon:	n/a	n/a
23	TAF1	chr7:140714241-140715298	PFSK-1	brain:	n/a	n/a
24	REST	chr7:140713618-140715530	H1-neurons	neurons:	n/a	n/a
25	BHLHE40	chr7:140714128-140715439	K562	blood:	n/a	chr7:140714918-140714934
26	TBL1XR1	chr7:140713648-140715490	K562	blood:	n/a	n/a
27	MAZ	chr7:140713683-140715677	IMR90	lung:	n/a	n/a
28	RAD21	chr7:140714258-140715332	SK-N-SH_RA	brain:	n/a	chr7:140714872-140714885
29	POLR2A	chr7:140713780-140715340	HepG2	liver:	n/a	n/a
30	POLR2A	chr7:140712968-140715384	GM12891	blood:	n/a	n/a
31	GTF2F1	chr7:140714472-140715326	K562	blood:	n/a	n/a
32	FOSL2	chr7:140714145-140715461	A549	lung:	n/a	n/a
33	TBP	chr7:140714131-140715322	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr7:140714267-140715467	K562	blood:	n/a	n/a
35	RELA	chr7:140714195-140715298	GM19193	blood:	n/a	n/a
36	RCOR1	chr7:140714522-140715309	K562	blood:	n/a	n/a
37	POLR2A	chr7:140713519-140715428	H1-hESC	embryonic stem cell:	n/a	n/a
38	GABPA	chr7:140713873-140715302	SK-N-SH	brain:	n/a	chr7:140714897-140714908 chr7:140714897-140714911 chr7:140714899-140714908 chr7:140714894-140714908
39	WRNIP1	chr7:140713690-140715340	GM12878	blood:	n/a	n/a
40	GABPA	chr7:140714048-140715449	SK-N-SH	brain:	n/a	chr7:140714897-140714908 chr7:140714897-140714911 chr7:140714899-140714908 chr7:140714894-140714908
41	ELK1	chr7:140714264-140715299	K562	blood:	n/a	n/a
42	NRF1	chr7:140713703-140715547	SK-N-SH	brain:	n/a	chr7:140714897-140714908 chr7:140714897-140714911 chr7:140714897-140714908 chr7:140714899-140714908 chr7:140714923-140714934 chr7:140714894-140714908
43	RAD21	chr7:140714631-140715376	HepG2	liver:	n/a	chr7:140714872-140714885
44	RELA	chr7:140713970-140715440	GM18505	blood:	n/a	n/a
45	POLR2A	chr7:140713853-140715510	PFSK-1	brain:	n/a	n/a
46	ATF2	chr7:140714118-140715335	GM12878	blood:	n/a	n/a
47	CTCF	chr7:140715280-140715430	SK-N-SH_RA	brain:	n/a	n/a
48	CREB1	chr7:140714153-140715318	HepG2	liver:	n/a	n/a
49	MYC	chr7:140713917-140715361	K562	blood:	n/a	n/a
50	REST	chr7:140713978-140715334	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:140715277-140715327	GM06990	blood:	n/a
2	chr7:140715277-140715327	NHBE	bronchial:	n/a
3	chr7:140715277-140715327	HepG2	liver:	n/a
4	chr7:140715277-140715327	SK-N-MC	brain:	n/a
5	chr7:140715277-140715327	RPTEC	kidney:	n/a
6	chr7:140715277-140715327	HNPCEpiC	eye:	n/a
7	chr7:140715277-140715327	HRE	kidney:	n/a
8	chr7:140715277-140715327	A549	lung:	n/a
9	chr7:140715277-140715327	Caco-2	colon:	n/a
10	chr7:140715277-140715327	SK-N-SH_RA	brain:	n/a
11	chr7:140715277-140715327	NH-A	brain:	n/a
12	chr7:140715277-140715327	GM12891	blood:	n/a
13	chr7:140715277-140715327	HUVEC	blood vessel:	n/a
14	chr7:140715277-140715327	HCF	heart:	n/a
15	chr7:140715277-140715327	SAEC	small airway:	n/a
16	chr7:140715277-140715327	HEEpiC	esophagus:	n/a
17	chr7:140715277-140715327	ovcar-3	ovarian:	n/a
18	chr7:140715277-140715327	PFSK-1	brain:	n/a
19	chr7:140715277-140715327	HRPEpiC	eye:	n/a
20	chr7:140715277-140715327	T-47D	breast:	n/a
21	chr7:140715277-140715327	NB4	blood:	n/a
22	chr7:140715277-140715327	HL-60	blood:	n/a
23	chr7:140715277-140715327	HMEC	breast:	n/a
24	chr7:140715277-140715327	HCT-116	colon:	n/a
25	chr7:140715277-140715327	AoSMC	blood vessel:	n/a
26	chr7:140715277-140715327	HAEpiC	amniotic membrane:	n/a
27	chr7:140715277-140715327	Jurkat	blood:	n/a
28	chr7:140715277-140715327	SK-N-SH	brain:	n/a
29	chr7:140715277-140715327	AG09309	skin:	n/a
30	chr7:140715277-140715327	GM19239	blood:	n/a
31	chr7:140715277-140715327	SKMC	muscle:	n/a
32	chr7:140715277-140715327	NHDF-neo	bronchial:	n/a
33	chr7:140715277-140715327	NT2-D1	testis:	n/a
34	chr7:140715277-140715327	HIPEpiC	eye:	n/a
35	chr7:140715277-140715327	K562	blood:	n/a
36	chr7:140715277-140715327	MCF-7	breast:	n/a
37	chr7:140715277-140715327	U87	brain:	n/a
38	chr7:140715277-140715327	AG09319	gingival:	n/a
39	chr7:140715277-140715327	Hela-S3	cervix:	n/a
40	chr7:140715277-140715327	AG04449	skin:	fetal
41	chr7:140715277-140715327	HCPEpiC	choroid plexus:	n/a
42	chr7:140715277-140715327	GM12892	blood:	n/a
43	chr7:140715277-140715327	PANC-1	pancreas:	n/a
44	chr7:140715277-140715327	AG10803	skin:	n/a
45	chr7:140715277-140715327	MCF10A-Er-Src	breast:	n/a
46	chr7:140715277-140715327	H1-hESC	embryonic stem cell:	embryo
47	chr7:140715277-140715327	HPAEpiC	pulmonary alveolar:	n/a
48	chr7:140715277-140715327	HEK293	kidney:	embryo
49	chr7:140715277-140715327	CMK	blood:	n/a
50	chr7:140715277-140715327	HRCEpiC	kidney:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140713242..140716757-chr7:140770540..140776348,9	MCF-7	breast:
2	chr7:140395386..140400852-chr7:140710628..140716984,11	MCF-7	breast:
3	chr7:140701133..140705248-chr7:140712773..140716152,4	K562	blood:
4	chr7:140621424..140625828-chr7:140713150..140716057,6	K562	blood:
5	chr7:140712784..140717043-chr7:140770770..140775163,8	MCF-7	breast:
6	chr7:140394845..140398499-chr7:140712009..140715919,6	MCF-7	breast:
7	chr7:140712651..140715864-chr7:141348079..141351599,5	MCF-7	breast:
8	chr7:140621424..140625988-chr7:140712136..140716057,7	K562	blood:
9	chr7:140394556..140398514-chr7:140712637..140716961,7	K562	blood:
10	chr7:140394719..140399884-chr7:140712014..140716961,9	K562	blood:

No data

Variant related genes	Relation type
MRPS33	TF binding region
MRPS33	CpG island
ENSG00000157764	Chromatin interaction
ENSG00000261115	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000006530	Chromatin interaction
ENSG00000273081	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10279193	0.83[EUR][1000 genomes]
rs1089265	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1091557	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764061	1.00[ASW][hapmap];0.81[YRI][hapmap]
rs12534351	0.83[EUR][1000 genomes]
rs12534354	0.83[EUR][1000 genomes]
rs1860481	0.85[EUR][1000 genomes]
rs2079829	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs246738	0.85[EUR][1000 genomes]
rs246740	0.85[EUR][1000 genomes]
rs246741	0.85[EUR][1000 genomes]
rs246742	0.85[EUR][1000 genomes]
rs246743	0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs246744	0.94[EUR][1000 genomes]
rs246745	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533300	1.00[JPT][hapmap]
rs3844322	0.83[EUR][1000 genomes]
rs38716	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38721	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs38724	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38725	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38727	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38728	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38733	0.82[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs38737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569881	1.00[ASW][hapmap];0.81[YRI][hapmap]
rs62486595	1.00[ASN][1000 genomes]
rs62486599	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949856	0.85[EUR][1000 genomes]
rs6950813	0.83[EUR][1000 genomes]
rs7778860	0.83[EUR][1000 genomes]
rs7782666	0.85[EUR][1000 genomes]
rs7787917	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791022	1.00[ASN][1000 genomes]
rs801118	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801119	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801122	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801124	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801126	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9640306	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs38743	EPHA1	cis	cerebellum	SCAN
rs38743	SVOPL	cis	cerebellum	SCAN
rs38743	TMEM178B	cis	Esophagus Mucosa	GTEx
rs38743	MRPS33	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140713000-140715400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:140713200-140715400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:140713400-140715400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:140713600-140715400	Active TSS	Colonic Mucosa	Colon
5	chr7:140713600-140715400	Active TSS	Fetal Muscle Trunk	muscle
6	chr7:140713600-140715400	Active TSS	Fetal Muscle Leg	muscle
7	chr7:140713600-140715400	Active TSS	Right Atrium	heart
8	chr7:140713600-140715400	Active TSS	Right Ventricle	heart
9	chr7:140713600-140715600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr7:140713600-140715600	Active TSS	GM12878-XiMat	blood
11	chr7:140713800-140715400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr7:140713800-140715400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:140713800-140715400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr7:140713800-140715400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:140713800-140715400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:140713800-140715400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:140713800-140715400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:140713800-140715400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:140713800-140715400	Active TSS	Aorta	Aorta
20	chr7:140713800-140715400	Active TSS	Fetal Intestine Large	intestine
21	chr7:140713800-140715400	Active TSS	Gastric	stomach
22	chr7:140713800-140715400	Active TSS	Ovary	ovary
23	chr7:140713800-140715400	Active TSS	Stomach Smooth Muscle	stomach
24	chr7:140713800-140715400	Active TSS	HSMM	muscle
25	chr7:140713800-140715400	Active TSS	HSMMtube	muscle
26	chr7:140713800-140715600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr7:140713800-140715600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:140713800-140715600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:140713800-140715600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:140713800-140715600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr7:140713800-140715600	Active TSS	A549	lung
32	chr7:140713800-140715600	Active TSS	NHDF-Ad	bronchial
33	chr7:140714000-140715400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:140714000-140715400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:140714000-140715400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:140714000-140715400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:140714000-140715400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:140714000-140715400	Active TSS	Fetal Brain Male	brain
39	chr7:140714000-140715400	Active TSS	Fetal Brain Female	brain
40	chr7:140714000-140715400	Active TSS	Fetal Heart	heart
41	chr7:140714000-140715400	Active TSS	Fetal Kidney	kidney
42	chr7:140714000-140715400	Active TSS	Fetal Lung	lung
43	chr7:140714000-140715400	Active TSS	Placenta	Placenta
44	chr7:140714000-140715400	Active TSS	Fetal Stomach	stomach
45	chr7:140714000-140715400	Active TSS	Left Ventricle	heart
46	chr7:140714000-140715400	Active TSS	Pancreas	Pancrea
47	chr7:140714000-140715400	Active TSS	Psoas Muscle	Psoas
48	chr7:140714000-140715400	Active TSS	Rectal Smooth Muscle	rectum
49	chr7:140714000-140715400	Active TSS	Thymus	Thymus
50	chr7:140714000-140715400	Bivalent/Poised TSS	HepG2	liver

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