Variant report

Variant	rs4234633
Chromosome Location	chr3:52557038-52557039
allele	C/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	chr3:52556890-52557988	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr3:52556474-52557063	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:52557034-52559033	K562	blood:	n/a	n/a
4	POLR2A	chr3:52556932-52559145	K562	blood:	n/a	n/a
5	POLR2A	chr3:52556753-52557132	U87	brain:	n/a	n/a
6	POLR2A	chr3:52556841-52557039	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:52556703-52560542	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52556659-52558161	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
2	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
3	chr3:52555579..52557218-chr3:52564676..52566664,2	MCF-7	breast:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1010552	0.85[ASN][1000 genomes]
rs1010554	0.81[ASN][1000 genomes]
rs1133415	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709284	0.87[ASN][1000 genomes]
rs11711421	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489732	0.94[ASN][1000 genomes]
rs12489828	0.88[ASN][1000 genomes]
rs13059862	0.89[ASN][1000 genomes]
rs13060048	0.89[ASN][1000 genomes]
rs13063160	0.89[ASN][1000 genomes]
rs13076398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081028	0.87[ASN][1000 genomes]
rs13303	0.87[ASN][1000 genomes]
rs13621	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1570	0.90[ASN][1000 genomes]
rs17052256	0.90[ASN][1000 genomes]
rs17052259	0.90[ASN][1000 genomes]
rs1821879	0.87[ASN][1000 genomes]
rs1961958	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1961959	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2015971	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2251219	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289249	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28661185	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2878628	0.90[ASN][1000 genomes]
rs33964154	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34005367	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796353	0.90[ASN][1000 genomes]
rs4282054	0.88[ASN][1000 genomes]
rs4434138	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4475032	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687624	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62256903	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445528	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778735	0.87[ASN][1000 genomes]
rs6778844	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6786043	0.86[ASN][1000 genomes]
rs6786919	0.89[ASN][1000 genomes]
rs6788887	0.89[ASN][1000 genomes]
rs6788993	0.89[ASN][1000 genomes]
rs6798246	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7614981	0.88[ASN][1000 genomes]
rs7636227	0.88[ASN][1000 genomes]
rs7638808	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9758945	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers 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 miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4234633	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs4234633	ITIH4-AS1	cis	Whole Blood	GTEx
rs4234633	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs4234633	MUSTN1	cis	Artery Aorta	GTEx
rs4234633	NT5DC2	cis	multi-tissue	Pritchard
rs4234633	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:52533400-52559800	Weak transcription	Liver	Liver
4	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52542000-52557400	Weak transcription	Thymus	Thymus
10	chr3:52544000-52557400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52550800-52558400	Strong transcription	HUVEC	blood vessel
13	chr3:52552000-52560800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:52552400-52559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52552600-52558200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:52552800-52557600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52552800-52557600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52552800-52557800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:52552800-52557800	Weak transcription	NHEK	skin
20	chr3:52552800-52558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:52552800-52560600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:52552800-52561200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:52552800-52562000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:52552800-52565400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
26	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:52553000-52558400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:52553000-52558400	Strong transcription	Lung	lung
29	chr3:52553200-52557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:52553200-52557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:52553200-52557800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:52553200-52557800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:52553200-52557800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:52553200-52558000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:52553200-52558000	Weak transcription	Osteobl	bone
36	chr3:52553200-52558400	Weak transcription	A549	lung
37	chr3:52553200-52559400	Weak transcription	Brain Anterior Caudate	brain
38	chr3:52553400-52557200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:52553400-52557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:52553400-52557400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:52553400-52557400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:52553400-52557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:52553400-52557400	Weak transcription	Ovary	ovary
44	chr3:52553400-52558000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:52553400-52558200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:52553400-52558200	Weak transcription	HepG2	liver
47	chr3:52553400-52558400	Strong transcription	Adipose Nuclei	Adipose
48	chr3:52553400-52558600	Weak transcription	Pancreas	Pancrea
49	chr3:52553600-52557200	Strong transcription	Right Ventricle	heart
50	chr3:52553600-52557800	Strong transcription	Fetal Stomach	stomach

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