Variant report

Variant	rs58339610
Chromosome Location	chr3:49845006-49845007
allele	A/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	POLR2A	chr3:49844642-49845256	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr3:49844752-49845138	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:49844762-49845731	GM12878	blood:	n/a	n/a
4	MAZ	chr3:49844935-49845251	GM12878	blood:	n/a	n/a
5	MAX	chr3:49844960-49845162	GM12878	blood:	n/a	n/a
6	NFIC	chr3:49844737-49845235	GM12878	blood:	n/a	n/a
7	EP300	chr3:49844911-49845035	K562	blood:	n/a	n/a
8	POLR2A	chr3:49839914-49845521	HUVEC	blood vessel:	n/a	n/a
9	TCF12	chr3:49844874-49845220	GM12878	blood:	n/a	n/a
10	ELF1	chr3:49844761-49845334	GM12878	blood:	n/a	chr3:49844985-49844998
11	TCF12	chr3:49844880-49845169	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49844761-49845033	HUVEC	blood vessel:	n/a	n/a
13	RELA	chr3:49844919-49845339	GM19099	blood:	n/a	n/a
14	POLR2A	chr3:49844903-49845340	K562	blood:	n/a	n/a
15	POLR2A	chr3:49844906-49845368	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:49842242-49845414	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr3:49842141-49845240	HUVEC	blood vessel:	n/a	n/a
18	EBF1	chr3:49844946-49845375	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49844984-49845766	GM12892	blood:	n/a	n/a
20	TCF3	chr3:49844829-49845190	GM12878	blood:	n/a	chr3:49845110-49845120
21	POLR2A	chr3:49844683-49845170	SK-N-MC	brain:	n/a	n/a
22	SIN3AK20	chr3:49844879-49845116	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr3:49844980-49845934	GM12892	blood:	n/a	n/a
24	EP300	chr3:49844755-49845115	SK-N-SH_RA	brain:	n/a	n/a
25	NFIC	chr3:49844765-49845342	GM12878	blood:	n/a	n/a
26	ELF1	chr3:49844782-49845152	K562	blood:	n/a	chr3:49844985-49844998
27	PML	chr3:49844618-49845345	GM12878	blood:	n/a	n/a
28	BHLHE40	chr3:49844958-49845128	GM12878	blood:	n/a	n/a
29	CHD2	chr3:49844974-49845083	GM12878	blood:	n/a	n/a
30	MTA3	chr3:49839849-49845759	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:49839942-49845851	GM12892	blood:	n/a	n/a
32	EP300	chr3:49844817-49845147	SK-N-SH_RA	brain:	n/a	n/a
33	MAX	chr3:49844366-49845170	NB4	blood:	n/a	chr3:49844545-49844555
34	FOXP2	chr3:49844876-49845145	SK-N-MC	brain:	n/a	n/a
35	MYC	chr3:49842630-49845224	NB4	blood:	n/a	chr3:49844545-49844555
36	STAT5A	chr3:49843182-49845298	GM12878	blood:	n/a	chr3:49843958-49843970 chr3:49844440-49844452 chr3:49844095-49844107
37	RUNX3	chr3:49844461-49845471	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:49844959-49846010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:

Variant related genes	Relation type
UBA7	TF binding region
MIR5193	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11130217	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs1491985	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1996664	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28535523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55924524	1.00[ASN][1000 genomes]
rs55997059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59357103	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59684465	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61557789	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6804970	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7613603	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648652	1.00[ASN][1000 genomes]
rs7649428	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851651	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs58339610	AMT	cis	lung	GTEx
rs58339610	NICN1	cis	Thyroid	GTEx
rs58339610	AMT	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841400-49845200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:49841400-49845800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
3	chr3:49841400-49845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr3:49841400-49846400	Weak transcription	Ovary	ovary
5	chr3:49841400-49847000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:49841600-49845400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:49841600-49845600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:49841600-49845800	Enhancers	Dnd41	blood
9	chr3:49841600-49846000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:49841600-49846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
12	chr3:49841800-49845400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:49841800-49845400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:49841800-49845600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:49841800-49845600	Enhancers	Left Ventricle	heart
16	chr3:49841800-49845800	Enhancers	Right Atrium	heart
17	chr3:49842000-49845800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49842000-49845800	Enhancers	Right Ventricle	heart
19	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:49842200-49845600	Enhancers	Lung	lung
21	chr3:49842200-49846600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:49842600-49845200	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:49842600-49845400	Enhancers	NHLF	lung
24	chr3:49842600-49845600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:49842600-49846000	Enhancers	NHEK	skin
26	chr3:49842800-49845200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:49842800-49845200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:49842800-49845400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:49842800-49846000	Enhancers	Esophagus	oesophagus
30	chr3:49843000-49845200	Weak transcription	Pancreas	Pancrea
31	chr3:49843000-49845200	Enhancers	Thymus	Thymus
32	chr3:49843000-49845600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:49843200-49845400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:49843400-49845200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:49843400-49845200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:49843400-49845400	Enhancers	Fetal Intestine Large	intestine
37	chr3:49843400-49845600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:49843400-49845800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:49843400-49845800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:49843400-49845800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:49843400-49846000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:49843400-49846200	Enhancers	Fetal Heart	heart
43	chr3:49843400-49846400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:49843600-49845200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:49843600-49845400	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:49843600-49845400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:49843600-49845400	Enhancers	HepG2	liver
49	chr3:49843600-49845600	Enhancers	HUVEC	blood vessel
50	chr3:49843600-49846000	Genic enhancers	Fetal Intestine Small	intestine

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