Variant report

Variant	rs3734512
Chromosome Location	chr6:74104419-74104420
allele	A/C
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	MYC	chr6:74104417-74104672	MCF-7	breast:	n/a	chr6:74104490-74104500
2	REST	chr6:74104401-74105027	PANC-1	pancreas:	n/a	n/a
3	TCF7L2	chr6:74104256-74105065	PANC-1	pancreas:	n/a	chr6:74104842-74104856
4	EGR1	chr6:74104164-74104800	ECC-1	luminal epithelium:	n/a	chr6:74104424-74104437 chr6:74104486-74104497 chr6:74104485-74104498 chr6:74104467-74104480 chr6:74104349-74104359 chr6:74104422-74104432 chr6:74104348-74104358 chr6:74104487-74104497 chr6:74104493-74104503 chr6:74104485-74104498 chr6:74104485-74104498 chr6:74104336-74104351 chr6:74104485-74104498 chr6:74104487-74104497 chr6:74104485-74104499 chr6:74104344-74104357 chr6:74104337-74104350 chr6:74104484-74104499 chr6:74104486-74104497 chr6:74104488-74104497
5	CREB1	chr6:74104302-74104741	ECC-1	luminal epithelium:	n/a	n/a
6	EGR1	chr6:74104251-74104727	ECC-1	luminal epithelium:	n/a	chr6:74104424-74104437 chr6:74104486-74104497 chr6:74104485-74104498 chr6:74104467-74104480 chr6:74104349-74104359 chr6:74104422-74104432 chr6:74104348-74104358 chr6:74104487-74104497 chr6:74104493-74104503 chr6:74104485-74104498 chr6:74104485-74104498 chr6:74104336-74104351 chr6:74104485-74104498 chr6:74104487-74104497 chr6:74104485-74104499 chr6:74104344-74104357 chr6:74104337-74104350 chr6:74104484-74104499 chr6:74104486-74104497 chr6:74104488-74104497
7	MAX	chr6:74104275-74104896	MCF-7	breast:	n/a	chr6:74104490-74104500
8	USF1	chr6:74104293-74105040	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr6:74104272-74105085	MCF-7	breast:	n/a	n/a
10	MYC	chr6:74104374-74104968	MCF-7	breast:	n/a	chr6:74104490-74104500
11	MAX	chr6:74104205-74105096	ECC-1	luminal epithelium:	n/a	chr6:74104490-74104500
12	POLR2A	chr6:74103972-74105304	PANC-1	pancreas:	n/a	n/a
13	EGR1	chr6:74104326-74104783	MCF-7	breast:	n/a	chr6:74104424-74104437 chr6:74104486-74104497 chr6:74104485-74104498 chr6:74104467-74104480 chr6:74104349-74104359 chr6:74104422-74104432 chr6:74104348-74104358 chr6:74104487-74104497 chr6:74104493-74104503 chr6:74104485-74104498 chr6:74104485-74104498 chr6:74104336-74104351 chr6:74104485-74104498 chr6:74104487-74104497 chr6:74104485-74104499 chr6:74104344-74104357 chr6:74104337-74104350 chr6:74104484-74104499 chr6:74104486-74104497 chr6:74104488-74104497
14	MAX	chr6:74104240-74105129	ECC-1	luminal epithelium:	n/a	chr6:74104490-74104500
15	TCF12	chr6:74104225-74104922	ECC-1	luminal epithelium:	n/a	n/a
16	SRF	chr6:74104213-74104721	ECC-1	luminal epithelium:	n/a	n/a
17	SIN3AK20	chr6:74104143-74105266	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr6:74104015-74105265	PANC-1	pancreas:	n/a	n/a
19	EGR1	chr6:74104249-74104831	MCF-7	breast:	n/a	chr6:74104424-74104437 chr6:74104486-74104497 chr6:74104485-74104498 chr6:74104467-74104480 chr6:74104349-74104359 chr6:74104422-74104432 chr6:74104348-74104358 chr6:74104487-74104497 chr6:74104493-74104503 chr6:74104485-74104498 chr6:74104485-74104498 chr6:74104336-74104351 chr6:74104485-74104498 chr6:74104487-74104497 chr6:74104485-74104499 chr6:74104344-74104357 chr6:74104337-74104350 chr6:74104484-74104499 chr6:74104486-74104497 chr6:74104488-74104497
20	MAX	chr6:74104210-74105102	MCF-7	breast:	n/a	chr6:74104490-74104500
21	NFIC	chr6:74104280-74104779	ECC-1	luminal epithelium:	n/a	n/a
22	USF1	chr6:74104320-74105030	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr6:74104354-74105036	ECC-1	luminal epithelium:	n/a	n/a
24	MYC	chr6:74104323-74104979	MCF-7	breast:	n/a	chr6:74104490-74104500
25	POLR2A	chr6:74104262-74105146	MCF-7	breast:	n/a	n/a
26	TAF1	chr6:74104418-74105062	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr6:74104195-74105046	ECC-1	luminal epithelium:	n/a	n/a
28	SRF	chr6:74104198-74104848	MCF-7	breast:	n/a	n/a
29	EGR1	chr6:74104317-74104627	K562	blood:	n/a	chr6:74104424-74104437 chr6:74104486-74104497 chr6:74104485-74104498 chr6:74104467-74104480 chr6:74104349-74104359 chr6:74104422-74104432 chr6:74104348-74104358 chr6:74104487-74104497 chr6:74104493-74104503 chr6:74104485-74104498 chr6:74104485-74104498 chr6:74104336-74104351 chr6:74104485-74104498 chr6:74104487-74104497 chr6:74104485-74104499 chr6:74104344-74104357 chr6:74104337-74104350 chr6:74104484-74104499 chr6:74104486-74104497 chr6:74104488-74104497
30	POLR2A	chr6:74104301-74105107	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:74104388-74104438	NHBE	bronchial:	n/a
2	chr6:74104388-74104438	BE2_C	brain:	n/a
3	chr6:74104388-74104438	HepG2	liver:	n/a
4	chr6:74104388-74104438	HMEC	breast:	n/a
5	chr6:74104388-74104438	HRE	kidney:	n/a
6	chr6:74104388-74104438	Hela-S3	cervix:	n/a
7	chr6:74104388-74104438	ovcar-3	ovarian:	n/a
8	chr6:74104388-74104438	GM12892	blood:	n/a
9	chr6:74104388-74104438	PrEC	prostate:	n/a
10	chr6:74104388-74104438	GM12891	blood:	n/a
11	chr6:74104388-74104438	HNPCEpiC	eye:	n/a
12	chr6:74104388-74104438	HPAEpiC	pulmonary alveolar:	n/a
13	chr6:74104388-74104438	SK-N-MC	brain:	n/a
14	chr6:74104388-74104438	HAEpiC	amniotic membrane:	n/a
15	chr6:74104388-74104438	AG09319	gingival:	n/a
16	chr6:74104388-74104438	RPTEC	kidney:	n/a
17	chr6:74104388-74104438	SAEC	small airway:	n/a
18	chr6:74104388-74104438	AG10803	skin:	n/a
19	chr6:74104388-74104438	SK-N-SH	brain:	n/a
20	chr6:74104388-74104438	IMR90	lung:	fetal
21	chr6:74104388-74104438	A549	lung:	n/a
22	chr6:74104388-74104438	HCT-116	colon:	n/a
23	chr6:74104388-74104438	HCPEpiC	choroid plexus:	n/a
24	chr6:74104388-74104438	AG04450	lung:	fetal
25	chr6:74104388-74104438	HL-60	blood:	n/a
26	chr6:74104388-74104438	SKMC	muscle:	n/a
27	chr6:74104388-74104438	GM06990	blood:	n/a
28	chr6:74104388-74104438	GM19239	blood:	n/a
29	chr6:74104388-74104438	HRCEpiC	kidney:	n/a
30	chr6:74104388-74104438	Jurkat	blood:	n/a
31	chr6:74104388-74104438	AG09309	skin:	n/a
32	chr6:74104388-74104438	NHDF-neo	bronchial:	n/a
33	chr6:74104388-74104438	HCF	heart:	n/a
34	chr6:74104388-74104438	GM12878	blood:	n/a
35	chr6:74104388-74104438	U87	brain:	n/a
36	chr6:74104388-74104438	HRPEpiC	eye:	n/a
37	chr6:74104388-74104438	HUVEC	blood vessel:	n/a
38	chr6:74104388-74104438	HCM	heart:	n/a
39	chr6:74104388-74104438	NT2-D1	testis:	n/a
40	chr6:74104388-74104438	PANC-1	pancreas:	n/a
41	chr6:74104388-74104438	LNCaP	prostate:	n/a
42	chr6:74104388-74104438	NB4	blood:	n/a
43	chr6:74104388-74104438	H1-hESC	embryonic stem cell:	embryo
44	chr6:74104388-74104438	AG04449	skin:	fetal
45	chr6:74104388-74104438	AoSMC	blood vessel:	n/a
46	chr6:74104388-74104438	NH-A	brain:	n/a
47	chr6:74104388-74104438	PFSK-1	brain:	n/a
48	chr6:74104388-74104438	BJ	skin:	n/a
49	chr6:74104388-74104438	HEEpiC	esophagus:	n/a
50	chr6:74104388-74104438	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74099074..74102810-chr6:74103260..74106649,3	K562	blood:
2	6:73859137-73881637..6:74099986-74112890	GM12878	blood:
3	chr6:74102482..74106495-chr6:74159619..74163030,5	MCF-7	breast:
4	chr6:74101120..74105028-chr6:74169928..74173303,3	K562	blood:
5	6:74000304-74012200..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo
6	chr6:74103315..74106293-chr6:74362194..74365078,3	MCF-7	breast:
7	chr6:74019175..74020751-chr6:74101665..74105754,3	MCF-7	breast:

Variant related genes	Relation type
DDX43	TF binding region
ENSG00000238464	TF binding region
RPS6P8	TF binding region
DDX43	CpG island
ENSG00000238464	CpG island
RPS6P8	CpG island
ENSG00000234882	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000135314	Chromatin interaction
ENSG00000234025	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11961187	0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs11964808	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12662148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12663695	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12665048	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16883692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2280286	0.81[AMR][1000 genomes]
rs35097680	0.90[AFR][1000 genomes]
rs3734516	0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3757107	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs723402	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs930806	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs930807	0.96[AMR][1000 genomes]
rs930808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv830693	chr6:74049342-74216080	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3734512	DDX43	cis	lymphoblastoid	seeQTL
rs3734512	DDX43	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74099200-74110200	Weak transcription	Right Atrium	heart
2	chr6:74099400-74104600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:74099800-74104600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:74101800-74108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:74102000-74104600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:74102200-74105400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:74104000-74105200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:74104200-74104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:74104200-74105000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:74104200-74105200	Active TSS	Ovary	ovary
11	chr6:74104200-74105200	Active TSS	Stomach Smooth Muscle	stomach
12	chr6:74104400-74104600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr6:74104400-74104600	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:74104400-74104600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
15	chr6:74104400-74104800	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr6:74104400-74104800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:74104400-74104800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:74104400-74104800	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr6:74104400-74104800	Flanking Active TSS	Placenta	Placenta
20	chr6:74104400-74104800	ZNF genes & repeats	Lung	lung
21	chr6:74104400-74105000	Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:74104400-74105000	Active TSS	Primary T cells fromperipheralblood	blood
23	chr6:74104400-74105000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:74104400-74105000	Active TSS	Pancreas	Pancrea
25	chr6:74104400-74105000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr6:74104400-74105000	Active TSS	Thymus	Thymus

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