Variant report

Variant	rs3753292
Chromosome Location	chr1:169091466-169091467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169087780..169089721-chr1:169091214..169093379,2	MCF-7	breast:
2	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040501	0.90[CHB][hapmap]
rs10919064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919065	0.85[CEU][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1200150	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.98[ASN][1000 genomes]
rs1200151	0.98[ASN][1000 genomes]
rs1200157	0.81[AMR][1000 genomes]
rs1200159	0.81[AMR][1000 genomes]
rs1200160	0.88[CEU][hapmap]
rs12128513	0.84[EUR][1000 genomes]
rs12128543	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1320964	0.90[CHB][hapmap]
rs1892094	0.89[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2901029	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs35527028	0.90[CHB][hapmap]
rs3766033	0.90[CHB][hapmap]
rs3766034	0.90[CHB][hapmap]
rs3766038	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3766039	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766042	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs3766044	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs3820054	0.84[CHB][hapmap]
rs4656648	0.90[EUR][1000 genomes]
rs6427178	0.85[EUR][1000 genomes]
rs7517394	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7540067	0.91[CEU][hapmap];0.84[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3753292	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs3753292	FMO2	cis	parietal	SCAN
rs3753292	NME7	cis	Thyroid	GTEx

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	chr1:169081200-169091800	Strong transcription	Fetal Brain Female	brain
5	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:169082400-169097400	Weak transcription	Fetal Thymus	thymus
7	chr1:169083600-169094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:169084000-169094000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
11	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:169085600-169091800	Genic enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:169085600-169092400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:169085600-169094800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:169085600-169096600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:169085800-169094000	Weak transcription	Placenta	Placenta
17	chr1:169085800-169097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
19	chr1:169086200-169094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
22	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:169086600-169095400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:169087000-169092600	Genic enhancers	Brain Hippocampus Middle	brain
28	chr1:169087000-169093800	Weak transcription	Dnd41	blood
29	chr1:169087800-169093600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:169087800-169094400	Weak transcription	Colonic Mucosa	Colon
31	chr1:169088000-169093800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:169088000-169093800	Weak transcription	Fetal Kidney	kidney
33	chr1:169088400-169093600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:169088400-169093800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:169088600-169092800	Strong transcription	Fetal Stomach	stomach
36	chr1:169089200-169093400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:169089200-169096600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:169089400-169091600	Genic enhancers	Brain Inferior Temporal Lobe	brain
39	chr1:169089600-169091600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:169089600-169092200	Weak transcription	HMEC	breast
41	chr1:169089600-169093400	Weak transcription	NHEK	skin
42	chr1:169089600-169094600	Weak transcription	Osteobl	bone
43	chr1:169089600-169101600	Genic enhancers	A549	lung
44	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:169089800-169091800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:169089800-169092600	Strong transcription	Fetal Intestine Large	intestine
47	chr1:169089800-169093200	Weak transcription	NH-A	brain
48	chr1:169089800-169093600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:169089800-169093600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:169089800-169094400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links