Variant report

Variant	rs3803704
Chromosome Location	chr16:71318577-71318578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71315560..71317453-chr16:71317463..71319154,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1002252	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1018910	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12149475	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708908	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12918378	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12919927	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12929550	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13330156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1593135	0.93[ASN][1000 genomes]
rs2009763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs236000	0.81[CHD][hapmap]
rs236004	0.80[CHD][hapmap]
rs28673886	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883935	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096374	0.82[EUR][1000 genomes]
rs3114643	0.82[EUR][1000 genomes]
rs34832413	0.90[ASN][1000 genomes]
rs3826247	0.81[CHD][hapmap]
rs4324135	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419068	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4788786	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4788787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6416737	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499492	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713532	0.81[ASW][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap]
rs7187450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7195330	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8049333	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[ASN][1000 genomes]
rs8050933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8056169	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8059792	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8060653	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8061378	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062240	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8063629	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9927032	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9928675	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9936354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9941262	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1062426	chr16:71307180-71423400	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3803704	FHOD1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71306600-71322600	Weak transcription	Small Intestine	intestine
2	chr16:71307800-71318600	Weak transcription	Psoas Muscle	Psoas
3	chr16:71310400-71318800	Weak transcription	Thymus	Thymus
4	chr16:71315400-71321800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:71315600-71318800	Weak transcription	Fetal Heart	heart
6	chr16:71315800-71319000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:71315800-71319000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr16:71315800-71319000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr16:71315800-71322000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr16:71315800-71322200	Weak transcription	Right Ventricle	heart
11	chr16:71316000-71318600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr16:71316200-71318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:71316200-71318800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:71316200-71318800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:71316200-71318800	Weak transcription	Spleen	Spleen
16	chr16:71316200-71321000	Strong transcription	HSMM	muscle
17	chr16:71316200-71321400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr16:71316200-71321600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr16:71316400-71318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr16:71316400-71318800	Weak transcription	NHLF	lung
21	chr16:71316400-71318800	Weak transcription	Osteobl	bone
22	chr16:71316400-71319000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr16:71316400-71319000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:71316600-71321000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:71316600-71322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr16:71316600-71322600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr16:71316800-71320000	Strong transcription	Brain Germinal Matrix	brain
28	chr16:71316800-71320600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:71316800-71320600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr16:71316800-71320600	Strong transcription	Fetal Lung	lung
31	chr16:71316800-71321000	Strong transcription	Primary B cells from cord blood	blood
32	chr16:71316800-71321000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr16:71316800-71321000	Strong transcription	Left Ventricle	heart
34	chr16:71316800-71321400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr16:71316800-71321600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:71316800-71322000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:71316800-71322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr16:71317000-71318600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr16:71317000-71318800	Strong transcription	Dnd41	blood
40	chr16:71317000-71319400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr16:71317000-71319600	Strong transcription	GM12878-XiMat	blood
42	chr16:71317000-71320000	Strong transcription	Fetal Brain Female	brain
43	chr16:71317000-71320400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:71317000-71320600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr16:71317000-71320600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:71317000-71320600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:71317000-71320600	Strong transcription	Fetal Thymus	thymus
48	chr16:71317000-71320600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr16:71317000-71320800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr16:71317000-71321000	ZNF genes & repeats	Primary T cells from cord blood	blood

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