Variant report

Variant	rs1002252
Chromosome Location	chr16:71286676-71286677
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	chr16:71284904..71287123-chr16:71289658..71291171,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1018910	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12149475	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12708908	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12708909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12708911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12918378	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12919927	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12929550	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13330156	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1593135	0.91[ASN][1000 genomes]
rs2009763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288048	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs236000	0.81[CHD][hapmap]
rs236004	0.80[CHD][hapmap]
rs28673886	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2883935	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096374	0.85[EUR][1000 genomes]
rs3114643	0.86[EUR][1000 genomes]
rs34832413	0.85[ASN][1000 genomes]
rs3803704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826247	0.81[CHD][hapmap]
rs4324135	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4419068	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788786	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6416737	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499492	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499493	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713532	0.81[ASW][hapmap];1.00[JPT][hapmap]
rs7187450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7195330	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8049333	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs8050933	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8056169	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8059792	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8060653	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8061378	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8062240	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8063629	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9927032	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9928675	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9936354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941262	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1860	chr16:71269156-71313852	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3373759	chr16:71286451-71288599	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002252	FHOD1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71279400-71289000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71279600-71288800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:71283600-71288800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:71283800-71288800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr16:71283800-71289000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:71284800-71288600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:71285000-71288600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:71285000-71289000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr16:71285200-71288400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:71285200-71288600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:71285400-71288600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr16:71285400-71289200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr16:71285600-71288600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr16:71285600-71288600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr16:71285600-71289200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr16:71285800-71288600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr16:71286200-71288400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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