Variant report

Variant	rs9633334
Chromosome Location	chr1:169169856-169169857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158265	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10158861	0.91[AMR][1000 genomes]
rs10919065	0.87[CHD][hapmap]
rs10919088	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919102	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11800843	0.90[ASW][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.84[YRI][hapmap]
rs11808274	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs12023291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12025233	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12026996	0.90[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs12029853	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs12030320	1.00[YRI][hapmap]
rs12032783	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12033078	0.91[AMR][1000 genomes]
rs12036968	0.91[YRI][hapmap]
rs12037211	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12038609	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs12043489	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs12043545	0.91[AMR][1000 genomes]
rs12045202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046139	0.82[AMR][1000 genomes]
rs12047231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12129969	0.86[CHB][hapmap]
rs12691502	0.84[CHD][hapmap]
rs12724494	0.89[CHB][hapmap]
rs12728466	0.84[CHD][hapmap]
rs1415928	0.93[CEU][hapmap];0.84[AMR][1000 genomes]
rs1589113	0.92[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs16828170	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs2268048	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2901029	0.96[CHD][hapmap]
rs3766058	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766089	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3820058	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56341747	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58585501	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61806986	0.91[AMR][1000 genomes]
rs61808865	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61808914	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs61808915	0.91[AMR][1000 genomes]
rs6664272	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685556	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7521338	0.91[AMR][1000 genomes]
rs968304	0.90[CHD][hapmap]
rs9804101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988595	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs9633334	FMO9P	cis	parietal	SCAN
rs9633334	C1orf114	cis	parietal	SCAN
rs9633334	SCYL3	cis	parietal	SCAN
rs9633334	C1orf114	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169163600-169184000	Weak transcription	Ovary	ovary
3	chr1:169167200-169176400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:169167800-169186800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169168000-169183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169169000-169170200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169169400-169170200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:169169400-169170200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:169169600-169170000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:169169600-169170000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:169169600-169170000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:169169600-169170000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:169169600-169170200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:169169600-169171000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:169169600-169171200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:169169600-169172600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169169600-169175600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:169169800-169170000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:169169800-169170000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:169169800-169170400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:169169800-169171000	Enhancers	NH-A	brain
22	chr1:169169800-169172800	Enhancers	NHEK	skin
23	chr1:169169800-169173200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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