Variant report

Variant	rs3743602
Chromosome Location	chr16:75590113-75590114
allele	C/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	HMGN3	chr16:75589192-75590400	K562	blood:	n/a	n/a
2	POLR2A	chr16:75589845-75590517	HCT-116	colon:	n/a	n/a
3	EGR1	chr16:75590081-75590341	GM12878	blood:	n/a	chr16:75590244-75590253 chr16:75590241-75590254 chr16:75590241-75590255 chr16:75590242-75590256 chr16:75590242-75590253 chr16:75590241-75590254 chr16:75590244-75590254 chr16:75590240-75590255 chr16:75590241-75590254 chr16:75590241-75590254
4	MYBL2	chr16:75589603-75590575	HepG2	liver:	n/a	n/a
5	MAZ	chr16:75589785-75590565	GM12878	blood:	n/a	chr16:75590241-75590251
6	POLR2A	chr16:75589077-75590427	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr16:75589917-75590393	A549	lung:	n/a	n/a
8	POLR2A	chr16:75589017-75590511	GM12892	blood:	n/a	n/a
9	MAX	chr16:75588976-75590454	ECC-1	luminal epithelium:	n/a	chr16:75590241-75590251
10	RFX5	chr16:75589785-75590422	HepG2	liver:	n/a	chr16:75590176-75590191 chr16:75590176-75590191 chr16:75590176-75590191 chr16:75590178-75590193
11	POLR2A	chr16:75589081-75590560	HUVEC	blood vessel:	n/a	n/a
12	E2F6	chr16:75589114-75590503	A549	lung:	n/a	chr16:75590246-75590255 chr16:75589684-75589695
13	TAF1	chr16:75590071-75590484	SK-N-SH	brain:	n/a	n/a
14	RFX5	chr16:75589998-75590389	K562	blood:	n/a	chr16:75590176-75590191 chr16:75590176-75590191 chr16:75590176-75590191 chr16:75590178-75590193
15	CREB1	chr16:75588978-75590448	H1-hESC	embryonic stem cell:	n/a	n/a
16	HA-E2F1	chr16:75588958-75590570	MCF-7	breast:	n/a	chr16:75590246-75590255
17	RFX5	chr16:75588834-75590651	IMR90	lung:	n/a	chr16:75590176-75590191 chr16:75590176-75590191 chr16:75589225-75589234 chr16:75590176-75590191 chr16:75590178-75590193
18	MYC	chr16:75589672-75590298	H1-hESC	embryonic stem cell:	n/a	chr16:75590241-75590251
19	STAT1	chr16:75590040-75590507	GM12878	blood:	n/a	n/a
20	TAF1	chr16:75590078-75590411	K562	blood:	n/a	n/a
21	MAFK	chr16:75590003-75590469	Hela-S3	cervix:	n/a	n/a
22	SRF	chr16:75589958-75590249	GM12878	blood:	n/a	n/a
23	EGR1	chr16:75589781-75590562	HCT-116	colon:	n/a	chr16:75590244-75590253 chr16:75590241-75590254 chr16:75590241-75590255 chr16:75590242-75590256 chr16:75590242-75590253 chr16:75590241-75590254 chr16:75590244-75590254 chr16:75590240-75590255 chr16:75590241-75590254 chr16:75590241-75590254
24	MYC	chr16:75589016-75590499	K562	blood:	n/a	chr16:75590241-75590251
25	POLR2A	chr16:75589131-75590518	GM18505	blood:	n/a	n/a
26	YY1	chr16:75589923-75590405	SK-N-SH_RA	brain:	n/a	chr16:75590246-75590255 chr16:75590243-75590252
27	STAT5A	chr16:75589217-75590129	GM12878	blood:	n/a	chr16:75589648-75589660
28	E2F6	chr16:75589536-75590376	K562	blood:	n/a	chr16:75590246-75590255 chr16:75589684-75589695
29	POLR2A	chr16:75589007-75590627	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr16:75589997-75590281	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr16:75589123-75590417	NB4	blood:	n/a	chr16:75590241-75590251
32	CBX3	chr16:75588962-75590443	K562	blood:	n/a	n/a
33	CHD2	chr16:75589990-75590358	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr16:75589735-75590480	K562	blood:	n/a	n/a
35	MAX	chr16:75589061-75590317	A549	lung:	n/a	chr16:75590241-75590251
36	EGR1	chr16:75590107-75590339	GM12878	blood:	n/a	chr16:75590244-75590253 chr16:75590241-75590254 chr16:75590241-75590255 chr16:75590242-75590256 chr16:75590242-75590253 chr16:75590241-75590254 chr16:75590244-75590254 chr16:75590240-75590255 chr16:75590241-75590254 chr16:75590241-75590254
37	YY1	chr16:75589805-75590403	GM12891	blood:	n/a	chr16:75590246-75590255 chr16:75590243-75590252
38	POLR2A	chr16:75588888-75590521	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr16:75590029-75590420	HUVEC	blood vessel:	n/a	n/a
40	MYC	chr16:75590062-75590119	K562	blood:	n/a	n/a
41	MAX	chr16:75589080-75590535	HepG2	liver:	n/a	chr16:75590241-75590251
42	POLR2A	chr16:75589893-75590501	HCT-116	colon:	n/a	n/a
43	EP300	chr16:75590109-75590508	K562	blood:	n/a	n/a
44	MYC	chr16:75589966-75590151	GM12878	blood:	n/a	n/a
45	POLR2A	chr16:75589138-75590487	GM15510	blood:	n/a	n/a
46	SRF	chr16:75590046-75590256	GM12878	blood:	n/a	n/a
47	POLR2A	chr16:75589080-75590494	K562	blood:	n/a	n/a
48	POLR2A	chr16:75589090-75590420	ECC-1	luminal epithelium:	n/a	n/a
49	E2F6	chr16:75588988-75590296	H1-hESC	embryonic stem cell:	n/a	chr16:75590246-75590255 chr16:75589684-75589695
50	E2F4	chr16:75590035-75590399	MCF10A-Er-Src	breast:	n/a	chr16:75590246-75590255

No.	Distal block	Cell Line	Cell type
1	chr16:75588622..75597419-chr16:75598326..75606239,14	K562	blood:
2	chr12:122240395..122241119-chr16:75589970..75590470,2	NB4	blood:
3	chr16:75589583..75590159-chr3:42641596..42642441,2	Hela-S3	cervix:
4	chr16:75549961..75554189-chr16:75589462..75592660,4	K562	blood:
5	chr16:75589355..75592242-chr16:75608320..75611115,2	K562	blood:
6	chr16:75589928..75591467-chr16:75655261..75657250,2	K562	blood:
7	chr16:75496764..75498931-chr16:75589140..75591199,3	MCF-7	breast:
8	chr16:75588082..75590325-chr16:77223299..77225155,3	K562	blood:
9	chr16:75496580..75498737-chr16:75588829..75590831,2	MCF-7	breast:
10	chr16:75496858..75499850-chr16:75589381..75591063,2	K562	blood:
11	chr16:75549686..75552508-chr16:75588605..75590350,2	MCF-7	breast:
12	chr16:75586208..75590870-chr16:75596068..75600585,8	K562	blood:
13	chr16:75589371..75591308-chr16:75680950..75683874,2	K562	blood:
14	chr16:75589627..75590183-chr5:32312420..32313106,2	Hela-S3	cervix:
15	chr16:75465449..75469390-chr16:75587663..75590801,6	K562	blood:
16	chr16:75587953..75591056-chr16:75597056..75601894,6	MCF-7	breast:
17	chr16:75549723..75552104-chr16:75587869..75590374,4	MCF-7	breast:
18	chr16:75589604..75590145-chrX:23760858..23761653,2	Hela-S3	cervix:
19	chr16:75587027..75591762-chr16:75651045..75658145,7	K562	blood:
20	chr15:65133627..65134289-chr16:75589695..75590232,2	Hela-S3	cervix:
21	chr16:75589724..75591808-chr16:75655719..75657999,2	MCF-7	breast:
22	chr16:75588411..75591308-chr16:75680950..75683486,5	K562	blood:
23	chr16:75574262..75576234-chr16:75588612..75590836,2	MCF-7	breast:
24	chr16:75589388..75590260-chr6:27860868..27861371,2	Hela-S3	cervix:
25	chr16:75587491..75591972-chr16:75596703..75602966,17	MCF-7	breast:

Variant related genes	Relation type
TMEM231	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000249240	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000150712	Chromatin interaction
ENSG00000123130	Chromatin interaction
ENSG00000034713	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000261717	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000262583	Chromatin interaction
ENSG00000103111	Chromatin interaction
ENSG00000241839	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000153774	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000166822	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11149840	0.86[AMR][1000 genomes]
rs11641617	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11642669	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11645180	0.81[AMR][1000 genomes]
rs2242407	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2432619	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2550885	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2550886	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2550887	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2550910	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2550911	0.88[EUR][1000 genomes]
rs2550912	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572093	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2641799	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2641800	0.87[EUR][1000 genomes]
rs2641804	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2641805	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2641809	0.88[EUR][1000 genomes]
rs2650396	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2738793	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2738796	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2738801	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2738802	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2738808	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2738816	0.86[EUR][1000 genomes]
rs2738817	0.82[AMR][1000 genomes]
rs2738818	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2738819	0.88[EUR][1000 genomes]
rs3743601	0.81[ASN][1000 genomes]
rs3743604	0.81[AMR][1000 genomes]
rs3784932	0.81[AMR][1000 genomes]
rs4149500	0.86[AMR][1000 genomes]
rs4149501	0.84[AMR][1000 genomes]
rs4149504	0.84[AMR][1000 genomes]
rs4485400	0.86[AMR][1000 genomes]
rs7199936	0.88[EUR][1000 genomes]
rs7202717	0.84[AMR][1000 genomes]
rs8055668	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8061183	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
6	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv870450	chr16:75538457-75591359	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	diseases
10	nsv906929	chr16:75569739-75594918	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3743602	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs3743602	ADAT1	cis	Nerve Tibial	GTEx
rs3743602	ADAT1	cis	Muscle Skeletal	GTEx
rs3743602	ADAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs3743602	ADAT1	cis	Artery Tibial	GTEx
rs3743602	ADAT1	cis	Adipose Subcutaneous	GTEx
rs3743602	ADAT1	cis	Esophagus Muscularis	GTEx
rs3743602	ADAT1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75588400-75590600	Active TSS	Brain Anterior Caudate	brain
2	chr16:75588600-75590200	Active TSS	GM12878-XiMat	blood
3	chr16:75588600-75590400	Active TSS	K562	blood
4	chr16:75588600-75590400	Active TSS	NH-A	brain
5	chr16:75588600-75590600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:75588600-75590600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr16:75588600-75590600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr16:75588600-75590600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr16:75588600-75590600	Active TSS	Brain Germinal Matrix	brain
10	chr16:75588600-75590600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr16:75588600-75590800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr16:75588800-75590200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:75588800-75590200	Active TSS	Aorta	Aorta
14	chr16:75588800-75590400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr16:75588800-75590400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:75588800-75590400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:75588800-75590400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr16:75588800-75590400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr16:75588800-75590400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr16:75588800-75590400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:75588800-75590400	Active TSS	Brain Angular Gyrus	brain
22	chr16:75588800-75590400	Active TSS	Brain Hippocampus Middle	brain
23	chr16:75588800-75590400	Active TSS	Brain Substantia Nigra	brain
24	chr16:75588800-75590400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr16:75588800-75590400	Active TSS	Fetal Brain Male	brain
26	chr16:75588800-75590400	Active TSS	Fetal Brain Female	brain
27	chr16:75588800-75590400	Active TSS	Fetal Kidney	kidney
28	chr16:75588800-75590400	Active TSS	NHDF-Ad	bronchial
29	chr16:75588800-75590600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr16:75588800-75590600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:75588800-75590600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:75588800-75590600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:75588800-75590600	Active TSS	Brain Cingulate Gyrus	brain
34	chr16:75588800-75590600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr16:75588800-75590600	Active TSS	Fetal Stomach	stomach
36	chr16:75588800-75590600	Active TSS	Ovary	ovary
37	chr16:75588800-75590600	Active TSS	Right Atrium	heart
38	chr16:75588800-75590600	Active TSS	Right Ventricle	heart
39	chr16:75588800-75590600	Active TSS	NHLF	lung
40	chr16:75588800-75590800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr16:75588800-75590800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr16:75588800-75590800	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr16:75588800-75590800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr16:75589000-75590200	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr16:75589000-75590200	Active TSS	NHEK	skin
46	chr16:75589000-75590400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:75589000-75590400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:75589000-75590400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:75589000-75590400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr16:75589000-75590400	Active TSS	Colon Smooth Muscle	Colon

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