Variant report

Variant	rs3927373
Chromosome Location	chr4:69185154-69185155
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	IRF1	chr4:69184827-69185189	K562	blood:	n/a	chr4:69185061-69185071 chr4:69185057-69185071 chr4:69185171-69185187 chr4:69185059-69185072 chr4:69185178-69185188 chr4:69185177-69185188
2	POLR2A	chr4:69184146-69185869	K562	blood:	n/a	n/a
3	MAFK	chr4:69184874-69185188	HepG2	liver:	n/a	n/a
4	MAFF	chr4:69184896-69185162	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:69184205-69185899	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
YTHDC1	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10003465	0.91[EUR][1000 genomes]
rs11131746	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11735530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12331971	0.95[EUR][1000 genomes]
rs13145544	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1320797	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1406695	0.91[ASN][1000 genomes]
rs1406696	0.91[ASN][1000 genomes]
rs17089240	0.94[CEU][hapmap]
rs17089241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1715086	0.82[EUR][1000 genomes]
rs1730872	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730875	0.82[EUR][1000 genomes]
rs1880183	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919905	0.81[ASN][1000 genomes]
rs2140519	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319887	0.95[ASN][1000 genomes]
rs34032921	0.91[ASN][1000 genomes]
rs34186169	1.00[ASN][1000 genomes]
rs34223548	0.91[ASN][1000 genomes]
rs34282559	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34527218	0.91[ASN][1000 genomes]
rs34896019	0.91[ASN][1000 genomes]
rs35051311	1.00[ASN][1000 genomes]
rs3797007	0.86[ASN][1000 genomes]
rs4860292	1.00[ASN][1000 genomes]
rs4860927	1.00[ASN][1000 genomes]
rs4860928	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860930	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860932	0.91[ASN][1000 genomes]
rs4860933	0.91[ASN][1000 genomes]
rs4860934	0.91[ASN][1000 genomes]
rs4860935	0.91[ASN][1000 genomes]
rs6552179	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822778	0.95[ASN][1000 genomes]
rs7658151	0.95[ASN][1000 genomes]
rs7670560	0.91[MEX][hapmap]
rs7678448	0.93[EUR][1000 genomes]
rs953794	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs953795	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9990842	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3927373	UTP3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69176200-69203600	Strong transcription	Liver	Liver
2	chr4:69176200-69203600	Strong transcription	HSMM	muscle
3	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:69176400-69185200	Strong transcription	Primary B cells from cord blood	blood
6	chr4:69176400-69185200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr4:69176400-69185400	Strong transcription	Brain Germinal Matrix	brain
8	chr4:69176400-69185400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr4:69176400-69185600	Strong transcription	Brain Anterior Caudate	brain
10	chr4:69176400-69186000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:69176400-69186000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr4:69176400-69186000	Strong transcription	Adipose Nuclei	Adipose
13	chr4:69176400-69186200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:69176400-69188800	Strong transcription	GM12878-XiMat	blood
15	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:69176600-69185400	Strong transcription	Primary T cells from cord blood	blood
20	chr4:69176600-69185800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:69176600-69190200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:69176600-69198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
25	chr4:69176800-69185400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
29	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:69177400-69190000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:69177400-69204000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:69177600-69186000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:69177800-69185600	Strong transcription	HMEC	breast
35	chr4:69177800-69186000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:69177800-69201200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:69178000-69185200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:69178000-69185200	Strong transcription	NHDF-Ad	bronchial
40	chr4:69178000-69185800	Strong transcription	Colon Smooth Muscle	Colon
41	chr4:69178000-69185800	Strong transcription	Fetal Kidney	kidney
42	chr4:69178000-69186000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:69178000-69186200	Strong transcription	Osteobl	bone
44	chr4:69178000-69190600	Strong transcription	HUVEC	blood vessel
45	chr4:69178000-69203600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr4:69178000-69205000	Strong transcription	Dnd41	blood
47	chr4:69178200-69188000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:69178200-69189600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:69178200-69193200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:69178400-69187600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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