Variant report

Variant	rs10829156
Chromosome Location	chr10:18950555-18950556
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	chr10:18950275-18951108	K562	blood:	n/a	chr10:18950399-18950408 chr10:18950981-18950994
2	POLR2A	chr10:18950074-18951237	K562	blood:	n/a	n/a
3	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
4	POLR2A	chr10:18949923-18951350	HepG2	liver:	n/a	n/a
5	MAFK	chr10:18950540-18950942	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
7	POLR2A	chr10:18950486-18951025	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:18950108-18951270	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:18950080-18951470	HepG2	liver:	n/a	n/a
10	TBL1XR1	chr10:18950472-18950989	K562	blood:	n/a	n/a
11	GATA3	chr10:18950498-18950593	SH-SY5Y	brain:	n/a	n/a
12	POLR2A	chr10:18950523-18951059	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:18949169..18950743-chr10:20135931..20138598,2	MCF-7	breast:
2	chr10:18909074..18910706-chr10:18949247..18951149,2	K562	blood:
3	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: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10732437	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741086	1.00[CHB][hapmap]
rs10741120	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs10741131	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10764584	1.00[CHD][hapmap]
rs10764587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10764661	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828834	0.91[GIH][hapmap]
rs10828879	1.00[CHD][hapmap]
rs10828906	1.00[CHD][hapmap]
rs10829157	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829199	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917209	1.00[ASN][1000 genomes]
rs1917823	1.00[ASN][1000 genomes]
rs4316423	0.86[EUR][1000 genomes]
rs4338439	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456162	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4475830	1.00[ASN][1000 genomes]
rs4484992	1.00[CHB][hapmap]
rs4606373	1.00[ASN][1000 genomes]
rs4634984	1.00[ASN][1000 genomes]
rs4636555	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748476	1.00[CHB][hapmap]
rs4748479	1.00[ASN][1000 genomes]
rs4748493	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748494	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748502	0.88[EUR][1000 genomes]
rs4748504	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748505	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4748507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62636215	0.89[ASN][1000 genomes]
rs6482516	1.00[CHD][hapmap]
rs6482534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6482545	0.89[ASN][1000 genomes]
rs6482546	0.89[ASN][1000 genomes]
rs6482565	0.84[EUR][1000 genomes]
rs6482567	0.87[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075678	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7077786	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7081271	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs7081435	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082235	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7084709	0.90[EUR][1000 genomes]
rs7090926	0.89[ASN][1000 genomes]
rs7092437	1.00[CHB][hapmap]
rs7093907	1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095666	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7098721	1.00[ASN][1000 genomes]
rs7099307	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7100884	1.00[ASN][1000 genomes]
rs7895709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7895775	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7908550	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909552	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910506	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs7911922	1.00[ASN][1000 genomes]
rs7918933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7922241	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7923072	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181345	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9731044	0.83[EUR][1000 genomes];1.00[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Sudden cardiac arrest	21658281	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10829156	NSUN6	cis	parietal	SCAN
rs10829156	OLAH	cis	parietal	SCAN
rs10829156	NSUN6	cis	cerebellum	SCAN

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	chr10:18947000-18951200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr10:18947200-18950600	Active TSS	K562	blood
4	chr10:18947400-18950600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr10:18947400-18950600	Active TSS	Muscle Satellite Cultured Cells	--
6	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:18947800-18950600	Active TSS	NHLF	lung
8	chr10:18948000-18950600	Active TSS	NH-A	brain
9	chr10:18948800-18950600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:18948800-18950600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:18948800-18951200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:18949400-18950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:18949400-18950800	Active TSS	HepG2	liver
15	chr10:18949400-18951000	Enhancers	Primary B cells from peripheral blood	blood
16	chr10:18949400-18951200	Enhancers	Brain Substantia Nigra	brain
17	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
18	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:18949600-18950600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:18949600-18950800	Enhancers	Ovary	ovary
21	chr10:18949600-18951000	Enhancers	Primary B cells from cord blood	blood
22	chr10:18949600-18951000	Enhancers	Aorta	Aorta
23	chr10:18949600-18951000	Enhancers	Brain Anterior Caudate	brain
24	chr10:18949600-18951000	Enhancers	Esophagus	oesophagus
25	chr10:18949600-18951000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:18949600-18951200	Enhancers	Gastric	stomach
27	chr10:18949600-18951200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr10:18949600-18951400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr10:18949600-18951400	Enhancers	Brain Hippocampus Middle	brain
30	chr10:18949600-18951400	Enhancers	Colon Smooth Muscle	Colon
31	chr10:18949600-18951400	Enhancers	Fetal Brain Male	brain
32	chr10:18949600-18951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr10:18949600-18951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:18949600-18952400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr10:18949600-18952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:18949600-18953800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:18949600-18957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:18949800-18950600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr10:18949800-18950600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:18949800-18950600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr10:18949800-18950600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:18949800-18950600	Weak transcription	NHDF-Ad	bronchial
44	chr10:18949800-18950800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:18949800-18950800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr10:18949800-18950800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr10:18949800-18950800	Enhancers	Fetal Kidney	kidney
48	chr10:18949800-18950800	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr10:18949800-18951000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:18949800-18951000	Flanking Active TSS	Liver	Liver

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