Variant report

Variant	rs12022729
Chromosome Location	chr1:93495269-93495270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:93494819-93495291	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93493844..93495450-chr1:93525930..93527938,2	K562	blood:

Variant related genes	Relation type
ENSG00000251837	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11164860	0.84[ASN][1000 genomes]
rs11164861	0.88[ASN][1000 genomes]
rs12023767	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027025	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039256	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043007	0.81[CHB][hapmap]
rs12043577	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119421	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130551	0.88[ASN][1000 genomes]
rs12134501	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141895	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678778	0.96[ASN][1000 genomes]
rs2086312	0.86[ASN][1000 genomes]
rs2253595	0.92[ASN][1000 genomes]
rs2492898	0.99[ASN][1000 genomes]
rs2815417	0.89[JPT][hapmap]
rs2928183	0.87[ASN][1000 genomes]
rs4626900	0.99[ASN][1000 genomes]
rs4847227	0.95[ASN][1000 genomes]
rs485336	1.00[ASN][1000 genomes]
rs486370	0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs492054	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs492754	0.83[ASN][1000 genomes]
rs493980	0.83[JPT][hapmap]
rs496465	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs497540	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs504418	0.96[ASN][1000 genomes]
rs517856	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521527	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs524045	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536837	0.84[ASN][1000 genomes]
rs544051	0.82[ASN][1000 genomes]
rs544285	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs553396	0.84[ASN][1000 genomes]
rs557812	0.94[ASN][1000 genomes]
rs56320266	0.88[ASN][1000 genomes]
rs572131	0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs57478994	0.99[ASN][1000 genomes]
rs590296	0.96[ASN][1000 genomes]
rs591820	0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs591868	0.84[ASN][1000 genomes]
rs592751	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs638462	0.82[ASN][1000 genomes]
rs638958	0.82[ASN][1000 genomes]
rs664524	0.92[ASN][1000 genomes]
rs664852	0.93[ASN][1000 genomes]
rs6674738	0.84[ASN][1000 genomes]
rs680285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs808833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9787147	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12022729	FAM69A	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93488000-93504200	Enhancers	Fetal Thymus	thymus
2	chr1:93492400-93497600	Enhancers	Thymus	Thymus
3	chr1:93493600-93496000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr1:93493600-93496800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:93493800-93495800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:93493800-93495800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:93493800-93496200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:93494000-93495600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:93494000-93495800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:93494000-93496200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:93494000-93496200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:93494200-93495600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:93494200-93496400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:93494800-93495400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:93494800-93495400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:93494800-93495400	Enhancers	GM12878-XiMat	blood
17	chr1:93494800-93495600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:93494800-93495600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:93494800-93496000	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:93494800-93498800	Enhancers	Dnd41	blood
21	chr1:93495000-93495400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr1:93495000-93495600	Enhancers	Primary B cells from cord blood	blood
23	chr1:93495200-93498400	Weak transcription	Primary B cells from peripheral blood	blood

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