Variant report

Variant	rs2038022
Chromosome Location	chr1:166873417-166873418
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:166873258..166876208-chr1:167028001..167029917,2	MCF-7	breast:
2	chr1:166872284..166875188-chr1:167022097..167024593,2	MCF-7	breast:
3	chr1:166873225..166874998-chr1:166958198..166960984,2	K562	blood:

Variant related genes	Relation type
ENSG00000143194	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10918599	0.89[ASN][1000 genomes]
rs10918600	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10918603	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10918607	0.80[CHD][hapmap]
rs11576904	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578336	0.80[CHD][hapmap]
rs11579987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11583927	0.92[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11588176	0.88[ASN][1000 genomes]
rs1543313	0.92[EUR][1000 genomes]
rs2038020	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072740	0.92[EUR][1000 genomes]
rs2072742	0.83[ASN][1000 genomes]
rs2142615	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2223221	0.96[EUR][1000 genomes]
rs2235184	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2294220	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34381372	0.93[EUR][1000 genomes]
rs4656516	0.90[EUR][1000 genomes]
rs4657612	0.96[EUR][1000 genomes]
rs61815130	0.91[ASN][1000 genomes]
rs61815132	0.86[ASN][1000 genomes]
rs6427047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6427048	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677644	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs742048	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7513457	0.96[EUR][1000 genomes]
rs7520897	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7545806	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9633326	0.96[CEU][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2038022	APOA2	cis	cerebellum	SCAN
rs2038022	TBX19	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166867200-166876800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:166867800-166873600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:166870200-166875400	Enhancers	Placenta	Placenta
4	chr1:166871200-166873600	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:166871200-166873800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:166871200-166874800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:166871200-166875600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:166871400-166875200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:166871400-166876000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:166871600-166874600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:166871600-166874800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:166871800-166873800	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:166872200-166874800	Weak transcription	HMEC	breast
14	chr1:166872600-166874000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:166872800-166875000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:166872800-166877000	Weak transcription	GM12878-XiMat	blood
17	chr1:166873000-166877000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:166873000-166877000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:166873200-166877000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:166873200-166877000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:166873400-166873600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:166873400-166873600	Bivalent Enhancer	HSMMtube	muscle
23	chr1:166873400-166874000	Enhancers	Fetal Heart	heart
24	chr1:166873400-166876600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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