Variant report

Variant	rs59357103
Chromosome Location	chr3:49890967-49890968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49882290..49886564-chr3:49889140..49892041,3	K562	blood:
2	chr3:49883594..49886564-chr3:49889140..49892041,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130217	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11709734	0.92[EUR][1000 genomes]
rs11720705	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12715437	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1491985	0.92[EUR][1000 genomes]
rs17598137	1.00[ASN][1000 genomes]
rs1799844	0.98[EUR][1000 genomes]
rs1996663	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1996664	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28535523	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35129566	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55997059	0.96[EUR][1000 genomes]
rs58339610	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59684465	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61557789	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260663	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62260720	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260723	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62262722	0.93[EUR][1000 genomes]
rs62262730	0.96[EUR][1000 genomes]
rs6790568	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804970	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809879	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613603	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7621797	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7628207	0.87[EUR][1000 genomes]
rs7637711	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649428	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9829155	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835157	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9836756	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9851651	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9870755	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	0.92[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59357103	AMT	cis	Thyroid	GTEx
rs59357103	NICN1	cis	Thyroid	GTEx
rs59357103	AMT	cis	lung	GTEx
rs59357103	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
3	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:49870200-49893000	Weak transcription	HSMM	muscle
6	chr3:49877000-49893000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
8	chr3:49877200-49893000	Weak transcription	Gastric	stomach
9	chr3:49877200-49893000	Weak transcription	NHDF-Ad	bronchial
10	chr3:49877200-49893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:49877400-49893000	Weak transcription	A549	lung
12	chr3:49877400-49893200	Weak transcription	Lung	lung
13	chr3:49877400-49893200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:49877600-49893200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:49877800-49893000	Weak transcription	Esophagus	oesophagus
16	chr3:49877800-49893000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:49879000-49893000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:49879000-49893000	Weak transcription	NHLF	lung
19	chr3:49879000-49893200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:49879200-49893000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:49879200-49893000	Weak transcription	Hela-S3	cervix
22	chr3:49879400-49893000	Weak transcription	HUVEC	blood vessel
23	chr3:49879400-49893000	Weak transcription	NH-A	brain
24	chr3:49879800-49893000	Weak transcription	Fetal Brain Male	brain
25	chr3:49880000-49893000	Weak transcription	Fetal Brain Female	brain
26	chr3:49880000-49893200	Weak transcription	Primary T cells from cord blood	blood
27	chr3:49880800-49893000	Weak transcription	Right Ventricle	heart
28	chr3:49880800-49893400	Weak transcription	Left Ventricle	heart
29	chr3:49881200-49893000	Weak transcription	Fetal Heart	heart
30	chr3:49881400-49892600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:49881800-49893000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:49882600-49893000	Weak transcription	Spleen	Spleen
33	chr3:49882800-49893400	Weak transcription	Pancreas	Pancrea
34	chr3:49883400-49893000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:49883400-49893000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:49883400-49893000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:49883400-49893200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:49883600-49893000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49883600-49893000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:49883600-49893000	Weak transcription	Osteobl	bone
41	chr3:49883800-49893000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:49883800-49893000	Weak transcription	K562	blood
43	chr3:49884000-49892400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49884000-49893000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:49884200-49891800	Weak transcription	HepG2	liver
46	chr3:49884200-49893000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:49884200-49893000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:49884200-49893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:49884200-49893000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:49884200-49893200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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