Variant report

Variant	rs10935341
Chromosome Location	chr3:139396758-139396759
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	RCOR1	chr3:139395695-139396932	K562	blood:	n/a	n/a
2	POLR2A	chr3:139396643-139396832	HepG2	liver:	n/a	n/a
3	RCOR1	chr3:139396086-139396790	K562	blood:	n/a	n/a
4	ZBTB7A	chr3:139396080-139396893	ECC-1	luminal epithelium:	n/a	n/a
5	ZBTB7A	chr3:139396250-139396933	K562	blood:	n/a	n/a
6	EGR1	chr3:139396754-139397124	K562	blood:	n/a	chr3:139396961-139396970 chr3:139396913-139396927
7	POLR2A	chr3:139396672-139396833	A549	lung:	n/a	n/a
8	MAZ	chr3:139396351-139397030	HepG2	liver:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
9	MAX	chr3:139396040-139396906	MCF-7	breast:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
10	MAZ	chr3:139396686-139396977	GM12878	blood:	n/a	n/a
11	USF1	chr3:139396146-139396905	HCT-116	colon:	n/a	chr3:139396473-139396484
12	POLR2A	chr3:139396011-139397093	K562	blood:	n/a	n/a
13	USF1	chr3:139396065-139396976	HCT-116	colon:	n/a	chr3:139396473-139396484
14	ZNF143	chr3:139396158-139396827	K562	blood:	n/a	n/a
15	MYC	chr3:139396026-139396988	K562	blood:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
16	E2F6	chr3:139396247-139396883	K562	blood:	n/a	chr3:139396873-139396883 chr3:139396386-139396401
17	USF1	chr3:139396185-139396812	K562	blood:	n/a	chr3:139396473-139396484
18	MYC	chr3:139396590-139396790	MCF10A-Er-Src	breast:	n/a	n/a
19	PML	chr3:139396539-139396860	K562	blood:	n/a	n/a
20	POLR2A	chr3:139396589-139396900	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:139395922-139396858	PBDE	blood:	n/a	n/a
22	POLR2A	chr3:139396672-139396817	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:139396697-139396790	ProgFib	skin:	n/a	n/a
24	MAX	chr3:139396175-139396894	A549	lung:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
25	MYC	chr3:139396619-139396779	K562	blood:	n/a	n/a
26	USF2	chr3:139396292-139396826	H1-hESC	embryonic stem cell:	n/a	chr3:139396473-139396484
27	MAX	chr3:139396587-139396840	K562	blood:	n/a	n/a
28	POLR2A	chr3:139396522-139396917	ECC-1	luminal epithelium:	n/a	n/a
29	HEY1	chr3:139396602-139396851	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:139396029-139396889	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:139396582-139396856	ECC-1	luminal epithelium:	n/a	n/a
32	SIN3A	chr3:139396248-139396821	H1-hESC	embryonic stem cell:	n/a	chr3:139396376-139396389 chr3:139396474-139396483 chr3:139396375-139396383 chr3:139396476-139396485
33	NR2F2	chr3:139396035-139397017	MCF-7	breast:	n/a	n/a
34	MAX	chr3:139396172-139396879	HepG2	liver:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
35	POLR2A	chr3:139396562-139396850	MCF10A-Er-Src	breast:	n/a	n/a
36	ARID3A	chr3:139396401-139396817	HepG2	liver:	n/a	n/a
37	NR2F2	chr3:139396579-139396898	K562	blood:	n/a	n/a
38	POLR2A	chr3:139396278-139396867	HCT-116	colon:	n/a	n/a
39	E2F6	chr3:139396138-139396855	K562	blood:	n/a	chr3:139396386-139396401
40	ZBTB7A	chr3:139396227-139396873	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr3:139396350-139396884	HCT-116	colon:	n/a	n/a
42	MAX	chr3:139396244-139396795	HepG2	liver:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
43	MAX	chr3:139396082-139396979	HepG2	liver:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
44	POLR2A	chr3:139396203-139396959	K562	blood:	n/a	n/a
45	POLR2A	chr3:139396472-139396887	HepG2	liver:	n/a	n/a
46	MYC	chr3:139396335-139396855	H1-hESC	embryonic stem cell:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486
47	HMGN3	chr3:139396230-139396847	K562	blood:	n/a	n/a
48	CBX3	chr3:139396149-139396794	K562	blood:	n/a	n/a
49	BHLHE40	chr3:139395980-139397115	K562	blood:	n/a	n/a
50	MYC	chr3:139396051-139396882	K562	blood:	n/a	chr3:139396474-139396485 chr3:139396470-139396489 chr3:139396475-139396484 chr3:139396477-139396486

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139395742..139397404-chr3:139400797..139402363,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBP1-5	chr3:139396547-139396846	NONHSAT092382
2	lnc-RBP1-5	chr3:139396547-139396760	NONHSAT092383

Variant related genes	Relation type
NMNAT3	TF binding region
ENSG00000261763	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12186041	0.96[ASN][1000 genomes]
rs12632145	0.87[ASN][1000 genomes]
rs12634170	0.96[ASN][1000 genomes]
rs13074121	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849303	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849305	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849307	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849309	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35449667	0.96[ASN][1000 genomes]
rs35657101	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922940	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4474999	0.81[ASN][1000 genomes]
rs4518082	0.96[ASN][1000 genomes]
rs4535184	0.96[ASN][1000 genomes]
rs4549242	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4615039	0.96[ASN][1000 genomes]
rs56711752	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57304307	0.96[ASN][1000 genomes]
rs59476496	0.91[ASN][1000 genomes]
rs62270189	0.87[ASN][1000 genomes]
rs62270193	0.87[ASN][1000 genomes]
rs62273120	0.93[ASN][1000 genomes]
rs62273121	0.93[ASN][1000 genomes]
rs62273122	0.91[ASN][1000 genomes]
rs6808215	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71627866	0.83[ASN][1000 genomes]
rs7617537	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636269	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7651551	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289581	0.96[ASN][1000 genomes]
rs9810042	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9810049	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815708	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833539	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836944	0.83[ASN][1000 genomes]
rs9848375	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9865942	0.96[ASN][1000 genomes]
rs9871543	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878498	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3431059	chr3:139395962-139398210	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10935341	NMNAT3	cis	Esophagus Muscularis	GTEx
rs10935341	NMNAT3	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139395200-139396800	Enhancers	Fetal Brain Male	brain
2	chr3:139395600-139397200	Active TSS	Primary T cells from cord blood	blood
3	chr3:139395600-139397200	Active TSS	Fetal Kidney	kidney
4	chr3:139395600-139397200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:139395800-139396800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:139395800-139396800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:139395800-139397200	Active TSS	Ovary	ovary
8	chr3:139395800-139397400	Active TSS	Brain Cingulate Gyrus	brain
9	chr3:139395800-139397400	Active TSS	Right Atrium	heart
10	chr3:139395800-139397800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:139396000-139396800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr3:139396000-139396800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr3:139396000-139396800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:139396000-139396800	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr3:139396000-139396800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:139396000-139396800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:139396000-139396800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:139396000-139396800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr3:139396000-139396800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr3:139396000-139396800	Active TSS	A549	lung
21	chr3:139396000-139396800	Active TSS	Hela-S3	cervix
22	chr3:139396000-139397200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr3:139396000-139397400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:139396000-139397400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:139396000-139397400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr3:139396000-139397400	Active TSS	Fetal Brain Female	brain
27	chr3:139396200-139396800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:139396200-139396800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:139396200-139396800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:139396200-139396800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:139396200-139396800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:139396200-139396800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:139396200-139396800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr3:139396200-139396800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:139396200-139396800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
36	chr3:139396200-139396800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:139396200-139396800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:139396200-139396800	Active TSS	Aorta	Aorta
39	chr3:139396200-139396800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
40	chr3:139396200-139396800	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:139396200-139396800	Active TSS	Esophagus	oesophagus
42	chr3:139396200-139396800	Active TSS	Gastric	stomach
43	chr3:139396200-139396800	Active TSS	Small Intestine	intestine
44	chr3:139396200-139396800	Bivalent/Poised TSS	HSMMtube	muscle
45	chr3:139396200-139396800	Bivalent/Poised TSS	NHLF	lung
46	chr3:139396200-139397000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:139396200-139397000	Active TSS	Psoas Muscle	Psoas
48	chr3:139396200-139397000	Active TSS	Stomach Smooth Muscle	stomach
49	chr3:139396200-139397200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr3:139396200-139397200	Active TSS	Brain Substantia Nigra	brain

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