Variant report

Variant	rs3766042
Chromosome Location	chr1:169092476-169092477
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169087780..169089721-chr1:169091214..169093379,2	MCF-7	breast:
2	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:
3	chr1:169087143..169088781-chr1:169092217..169094524,2	K562	blood:
4	chr1:169092445..169095068-chr1:169098832..169100908,2	K562	blood:
5	chr1:169087281..169089561-chr1:169092217..169094257,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1040502	0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.97[ASN][1000 genomes]
rs10919064	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10919065	0.85[CEU][hapmap]
rs1200160	0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12084793	0.81[YRI][hapmap]
rs12086665	0.83[LWK][hapmap]
rs12128513	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12128543	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1892094	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2420008	0.83[LWK][hapmap]
rs2901029	0.85[CEU][hapmap]
rs3753292	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs3766039	0.92[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3766044	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656648	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427178	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517394	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540067	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754549	0.93[ASN][1000 genomes]
rs754550	0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs754551	0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766042	FMO9P	cis	parietal	SCAN
rs3766042	NME7	cis	Thyroid	GTEx
rs3766042	FMO2	cis	parietal	SCAN
rs3766042	C1orf114	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169094600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169081000-169098200	Weak transcription	Small Intestine	intestine
4	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:169082400-169097400	Weak transcription	Fetal Thymus	thymus
6	chr1:169083600-169094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169084000-169094000	Weak transcription	Primary T cells from cord blood	blood
8	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
10	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:169085600-169094800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:169085600-169096600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:169085800-169094000	Weak transcription	Placenta	Placenta
14	chr1:169085800-169097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
16	chr1:169086200-169094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
19	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:169086600-169095400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:169087000-169092600	Genic enhancers	Brain Hippocampus Middle	brain
25	chr1:169087000-169093800	Weak transcription	Dnd41	blood
26	chr1:169087800-169093600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:169087800-169094400	Weak transcription	Colonic Mucosa	Colon
28	chr1:169088000-169093800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:169088000-169093800	Weak transcription	Fetal Kidney	kidney
30	chr1:169088400-169093600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:169088400-169093800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:169088600-169092800	Strong transcription	Fetal Stomach	stomach
33	chr1:169089200-169093400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:169089200-169096600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:169089600-169093400	Weak transcription	NHEK	skin
36	chr1:169089600-169094600	Weak transcription	Osteobl	bone
37	chr1:169089600-169101600	Genic enhancers	A549	lung
38	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:169089800-169092600	Strong transcription	Fetal Intestine Large	intestine
40	chr1:169089800-169093200	Weak transcription	NH-A	brain
41	chr1:169089800-169093600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:169089800-169093600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:169089800-169094400	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:169089800-169096200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:169090000-169093200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:169090000-169093400	Weak transcription	Brain Substantia Nigra	brain
47	chr1:169090000-169098200	Weak transcription	NHDF-Ad	bronchial
48	chr1:169090000-169098400	Weak transcription	HSMMtube	muscle
49	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:169090400-169092600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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