Variant report

Variant	rs4747356
Chromosome Location	chr10:18949837-18949838
allele	C/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	CEBPB	chr10:18949720-18950309	K562	blood:	n/a	n/a
2	CEBPB	chr10:18949760-18949876	HepG2	liver:	n/a	n/a
3	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
4	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
5	CEBPB	chr10:18949715-18950022	IMR90	lung:	n/a	n/a
6	POLR2A	chr10:18947179-18950099	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr10:18946825-18950010	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
2	chr10:18949169..18950743-chr10:20135931..20138598,2	MCF-7	breast:
3	chr10:18909074..18910706-chr10:18949247..18951149,2	K562	blood:
4	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ARL5B-AS1	TF binding region
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10741111	0.80[EUR][1000 genomes]
rs10764625	0.81[EUR][1000 genomes]
rs10828976	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11015259	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7081972	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4747356	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs4747356	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs4747356	RP11-499P20.2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18946800-18950600	Active TSS	GM12878-XiMat	blood
2	chr10:18947000-18950000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr10:18947000-18950000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr10:18947000-18950200	Active TSS	Colonic Mucosa	Colon
5	chr10:18947000-18950200	Active TSS	HSMM	muscle
6	chr10:18947000-18951200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr10:18947200-18950000	Active TSS	Left Ventricle	heart
8	chr10:18947200-18950200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:18947200-18950400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:18947200-18950600	Active TSS	K562	blood
11	chr10:18947400-18950000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:18947400-18950000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr10:18947400-18950000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:18947400-18950600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr10:18947400-18950600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:18947600-18950000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:18947600-18950000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr10:18947600-18950000	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr10:18947600-18950000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr10:18947600-18950000	Active TSS	Fetal Lung	lung
22	chr10:18947600-18950000	Active TSS	Hela-S3	cervix
23	chr10:18947600-18950000	Active TSS	HMEC	breast
24	chr10:18947600-18950200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr10:18947800-18950200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr10:18947800-18950400	Active TSS	HSMMtube	muscle
27	chr10:18947800-18950600	Active TSS	NHLF	lung
28	chr10:18948000-18950000	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr10:18948000-18950200	Active TSS	Osteobl	bone
30	chr10:18948000-18950600	Active TSS	NH-A	brain
31	chr10:18948800-18950200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr10:18948800-18950400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr10:18948800-18950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:18948800-18950600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:18948800-18950600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:18948800-18951200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:18949200-18950000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr10:18949400-18950400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:18949400-18950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:18949400-18950800	Active TSS	HepG2	liver
42	chr10:18949400-18951000	Enhancers	Primary B cells from peripheral blood	blood
43	chr10:18949400-18951200	Enhancers	Brain Substantia Nigra	brain
44	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
45	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr10:18949600-18950000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr10:18949600-18950000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr10:18949600-18950000	Enhancers	Fetal Heart	heart
49	chr10:18949600-18950200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr10:18949600-18950200	Enhancers	Primary hematopoietic stem cells	blood

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